Have you asked the CTO (or another engineer) about the history of the codebase? It certainly sounds like they were busy getting something working, with little time for niceties.
After getting a bit more background, then maybe you could suggest that since there are now paying customers, maintainability has gained significantly in importance, especially since the company has gained a much better idea of what works for the customers.
VoIP, web cam, chat, meeting rooms, open office, and more.
http://code.google.com/p/openqwaq/