Dein Beispiel funktioniert bei mir einwandfrei, es erscheint einfach "," zwischen den Zahlen.
In deinem Code habe ich trotzdem ein paar Sachen angemerkt:
%BRAUCHTS NICHT %\NeedsTeXFormat{LaTeX2e}[1995/06/01] 
\documentclass[ 
    BCOR12mm, 
    DIV18, 
    headsepline, 
    oneside, 
    idxtotoc, 
    bibtotoc, 
    liststotoc, 
    openany, 
    pointlessnumbers, 
    12pt 
    ] 
    {scrbook} 
\usepackage[ngerman]{babel} 
\usepackage[T1]{fontenc} 
\usepackage[latin1]{inputenc} 
\usepackage[babel,german=quotes]{csquotes} 
\usepackage{lmodern} 
\usepackage{float} 
\restylefloat{figure}                %für \begin{figure}[H] 
\usepackage{setspace} 
\usepackage{mathcomp} 
%WEGLASSEN! %\usepackage{ae}                          % Für PDF-Erstellung 
\usepackage[hang]{caption}              % mehrzeilige Captions ausrichten 
\usepackage[final]{graphicx}             % Bilder einbinden 
\usepackage{verbatim}                    % Für Quelltexte u.ä. 
\usepackage{cite}                        % Zitate [1,3,5,7,6] zu [1,2,5-7] zusammengefassen 
\usepackage{marvosym}                    % zur Darstellung des Eurosymbols \EUR 
\usepackage{makeidx}                     % für Erstellung der Indexdatei 
\usepackage{ifthen} 
\usepackage{miller}                      % zum Schreiben von Millerschen Indizees 
\usepackage{numprint}                    % zum Formatieren von Zahlen und Zahl und Einheit 
\usepackage{hhline}                      % erweiterte Möglichkeiten der Liniendarstellung 
\addto\extrasgerman{\sisetup{locale = DE}} 
\usepackage{siunitx}%für SI-Einheiten 
\sisetup{ 
per=frac 
,repeatunits = false 
,trapambigrange=false 
, tophrase = - 
,loctolang=DE:ngerman 
%,output-decimal-marker=comma 
,decimalsymbol=comma 
} 
\usepackage{amsmath} 
\usepackage{subfig} %Bilder nebeneinander 
\usepackage{hyperref}% MUSS IN 90% DER FÄLLE ALS ALLERLETZES PAKET GELADEN WERDEN       % URL verlinken, bzw. für Formatierung URL Adresse im Literaturverzeichnis 
\renewcommand{\sectionmark}[1]{\markright{\thesection\enskip #1}} 
\begin{document} 
\SI{0,57}{N \per\mm\squared} 
\end{document} 
Vielleicht liegt es an veralteten Paketen? Stell ein \listfiles noch vor \documentclass{...}, dann werden im .log-file die verwendeten Pakete und Versionen aufgelistet.
Bei mir sieht das mit dem Code oben so aus:
 *File List*
 scrbook.cls    2009/07/24 v3.04a KOMA-Script document class (book)
scrkbase.sty    2009/07/24 v3.04a KOMA-Script package (KOMA-Script-dependent ba
sics and keyval usage)
 scrbase.sty    2009/07/24 v3.04a KOMA-Script package (KOMA-Script-independent 
basics and keyval usage)
  keyval.sty    1999/03/16 v1.13 key=value parser (DPC)
scrlfile.sty    2009/03/25 v3.03 KOMA-Script package (loading files)
tocbasic.sty    2009/06/08 v3.03b KOMA-Script package (handling toc-files)
scrsize12pt.clo    2009/07/24 v3.04a KOMA-Script font size class option (12pt)
typearea.sty    2009/07/24 v3.04a KOMA-Script package (type area)
   babel.sty    2008/07/06 v3.8l The Babel package
ngermanb.ldf    2008/07/06 v2.6n new German support from the babel system
 fontenc.sty
   t1enc.def    2005/09/27 v1.99g Standard LaTeX file
inputenc.sty    2008/03/30 v1.1d Input encoding file
  latin1.def    2008/03/30 v1.1d Input encoding file
csquotes.sty    2009/09/23 v4.4c context-sensitive quotations
etoolbox.sty    2009/08/06 v1.8 e-TeX tools for LaTeX
    etex.sty    1998/03/26 v2.0 eTeX basic definition package (PEB)
csquotes.def    2009/09/23 v4.4c csquotes generic definitions
csquotes.cfg    2009/05/30 v4.4 csquotes configuration
 lmodern.sty    2009/10/30 v1.6 Latin Modern Fonts
   float.sty    2001/11/08 v1.3d Float enhancements (AL)
setspace.sty    2000/12/01 6.7 Contributed and Supported LaTeX2e package
mathcomp.sty    2001/01/07 v0.1f (TBo)
textcomp.sty    2005/09/27 v1.99g Standard LaTeX package
  ts1enc.def    2001/06/05 v3.0e (jk/car/fm) Standard LaTeX file
 caption.sty    2009/10/09 v3.1k Customizing captions (AR)
caption3.sty    2009/10/09 v3.1k caption3 kernel (AR)
graphicx.sty    1999/02/16 v1.0f Enhanced LaTeX Graphics (DPC,SPQR)
graphics.sty    2009/02/05 v1.0o Standard LaTeX Graphics (DPC,SPQR)
    trig.sty    1999/03/16 v1.09 sin cos tan (DPC)
graphics.cfg    2009/08/28 v1.8 graphics configuration of TeX Live
  pdftex.def    2009/08/25 v0.04m Graphics/color for pdfTeX
verbatim.sty    2003/08/22 v1.5q LaTeX2e package for verbatim enhancements
    cite.sty    2009/08/29  v 5.2
marvosym.sty    2006/05/11 v2.1 Martin Vogel's Symbols font definitions
 makeidx.sty    2000/03/29 v1.0m Standard LaTeX package
  ifthen.sty    2001/05/26 v1.1c Standard LaTeX ifthen package (DPC)
  miller.sty    2004/09/20 v1.2 print miller indices
numprint.sty    2008/02/17 v1.38 Print numbers (HH)
   array.sty    2008/09/09 v2.4c Tabular extension package (FMi)
  hhline.sty    1994/05/23 v2.03 Table rule package (DPC)
 siunitx.sty    2009/09/21 v1.3a A comprehensive (SI) units package
 xkeyval.sty    2008/08/13 v2.6a package option processing (HA)
 xkeyval.tex    2008/08/13 v2.6a key=value parser (HA)
 amstext.sty    2000/06/29 v2.01
  amsgen.sty    1999/11/30 v2.0
  xspace.sty    2006/05/08 v1.12 Space after command names (DPC,MH)
si-prefix.cfg    2009/09/21 v1.3a siunitx: SI Multiple prefixes
si-named.cfg    2009/09/21 v1.3a siunitx: SI Named units
 si-addn.cfg    2009/09/21 v1.3a siunitx: SI Additional units
si-prefixed.cfg    2009/09/21 v1.3a siunitx: SI Prefixed units
si-accepted.cfg    2009/09/21 v1.3a siunitx: SI Accepted units
si-physical.cfg    2009/09/21 v1.3a siunitx: SI Physically-measured units
 si-abbr.cfg    2009/09/21 v1.3a siunitx: Abbreviated units
   si-DE.cfg    2009/09/21 v1.3a siunitx: Germany locale
 amsmath.sty    2000/07/18 v2.13 AMS math features
  amsbsy.sty    1999/11/29 v1.2d
  amsopn.sty    1999/12/14 v2.01 operator names
  subfig.sty    2005/06/28 ver: 1.3 subfig package
hyperref.sty    2009/10/09 v6.79a Hypertext links for LaTeX
   ifpdf.sty    2009/04/10 v2.0 Provides the ifpdf switch (HO)
  ifvtex.sty    2008/11/04 v1.4 Switches for detecting VTeX and its modes (HO)
 ifxetex.sty    2009/01/23 v0.5 Provides ifxetex conditional
 hycolor.sty    2009/10/02 v1.5 Code for color options of hyperref/bookmark (HO
)
xcolor-patch.sty    2009/10/02 xcolor patch
  pd1enc.def    2009/10/09 v6.79a Hyperref: PDFDocEncoding definition (HO)
etexcmds.sty    2007/12/12 v1.2 Prefix for e-TeX command names (HO)
infwarerr.sty    2007/09/09 v1.2 Providing info/warning/message (HO)
hyperref.cfg    2002/06/06 v1.2 hyperref configuration of TeXLive
kvoptions.sty    2009/08/13 v3.4 Keyval support for LaTeX options (HO)
kvsetkeys.sty    2009/07/30 v1.5 Key value parser with default handler support 
(HO)
     url.sty    2006/04/12  ver 3.3  Verb mode for urls, etc.
  bitset.sty    2007/09/28 v1.0 Data type bit set (HO)
 intcalc.sty    2007/09/27 v1.1 Expandable integer calculations (HO)
bigintcalc.sty    2007/11/11 v1.1 Expandable big integer calculations (HO)
pdftexcmds.sty    2009/09/23 v0.6 LuaTeX support for pdfTeX utility functions (
HO)
ifluatex.sty    2009/04/17 v1.2 Provides the ifluatex switch (HO)
 ltxcmds.sty    2009/08/05 v1.0 Some LaTeX kernel commands for general use (HO)
atbegshi.sty    2008/07/31 v1.9 At begin shipout hook (HO)
 hpdftex.def    2009/10/09 v6.79a Hyperref driver for pdfTeX
  ts1cmr.fd    1999/05/25 v2.5h Standard LaTeX font definitions
   t1lmr.fd    2009/10/30 v1.6 Font defs for Latin Modern
supp-pdf.mkii
 nameref.sty    2007/05/29 v2.31 Cross-referencing by name of section
refcount.sty    2008/08/11 v3.1 Data extraction from references (HO)
  Test-3.out
  Test-3.out
  ot1lmr.fd    2009/10/30 v1.6 Font defs for Latin Modern
  omllmm.fd    2009/10/30 v1.6 Font defs for Latin Modern
 omslmsy.fd    2009/10/30 v1.6 Font defs for Latin Modern
 omxlmex.fd    2009/10/30 v1.6 Font defs for Latin Modern
 ot1lmss.fd    2009/10/30 v1.6 Font defs for Latin Modern
 ot1lmtt.fd    2009/10/30 v1.6 Font defs for Latin Modern
 ***********
Mach das mal bei dir und vergleiche die Versionen. Es sind übrigens so viele Pakete, weil du kein wirklich minimales Beispiel gemacht hast.