Bumping this as the same thing happened to me. All text messages suddenly disappeared.
I had auto-delete on but my text message limit per conversation was not nearly reached (was 2000 per conversation). All I can say is one conversation was around 1000 texts...might have been over already but I don't know. I checked and I have plenty of space available on the phone and sd card (phone is relatively stock).
This was with the stock messaging app. I downloaded Handcent and it only sees what the stock messaging app sees (2 messages).
Any suggestions? I suppose the texts are gone forever but I have no idea why it happened.