I managed to do this, I will document it here for future reference.

In the C:\Program Files (x86)\Microsoft Office\Office12\Bibliography\Style\ISO690Nmerical.XSL file, there's two templates, named templ_prop_OpenBracket and templ_prop_CloseBracket. These get the actual bracket from some other XML source but I can't find where that's stored. Not in the .docx file as far as I can tell. So I just changed the XSL file. I changed line 2013 and 2024 to <xsl:text>[</xsl:text> and <xsl:text>]</xsl:text> respectively, and that did the job.

Come on MS, surely there's a better way to do this which I'm missing somehow...