Preserving thousands separator with siunitx

This is described in section 5.6 Printing numbers of the manual (for v. 2.5s, dated 2013/07/31). The group-separator key defines the separator between groups of digits. By default grouping is not applied for numbers with four digits (e.g. 9000), so there's no need to do anything for that. (This can be changed with group-minimum-digits, which defines how many digits must be present for grouping to apply.)

\documentclass[12pt]{article}
\usepackage{siunitx}
\sisetup{group-separator = {,}}
\begin{document}
\SI{9000}{\m}

\SI{90000}{\m}

\end{document}