1) Fairly low budget, virtually no paid advertising,
2) Michigan, Killer7, and Contact all got overseas publication deals that did alright for him even if not for the publishers.
3) Grasshopper developed a few for-profit titles to help fund Suda's money-losers. Shining Soul for GBA was developed by Grasshopper for SEGA.
4) Grasshopper also does sound design and music for other companies; mostly shovelware, Simple2000 stuff, etc.
GamerWiki has Grasshopper as founded with only 10million yen capital, which is about 100k dollars. So obviously there's been investment since then or the combination of the four previously mentioned factors have been enough to keep the company going. He's got 40 employees or something working for him (GamerWiki says 30 but that's outdated.)
Unlike the movie industry, video game publishers don't fund loss leaders for critical acclaim--which, by the way, Suda doesn't get a lot of from the vast majority of media. They fund loss leaders for research, but Grasshopper as such shoddy programmers that I highly doubt there's most salvageable tech from any of Suda's stuff.