I don't know if there's a limit, but that's the right place for your saves. I just checked mine and I have a ton of saves in there, so it would appear you may be experiencing some kind of glitch. You sure you have enough space on your drive?
Yes, I have more than 200Gb available, the entire gamesaves folder is only 3.36Mb.
I just checked if I had steamcloud enabled and it seems I do, there are a lot of saves in L:\Steam\userdata\54782079\20920\remote but none past a certain point. I think it might have been the steamcloud limit of 100Mb that didn't allow any more saves.
According to Dan Forever in a post he made yesterday
the old saves should have been replaced with newer ones when I reach the limit.
In the Steam library, if you right click->properties and go to the "updates" tab, you'll see how much space you have available for storing files on steam cloud. When you reach this limit, don't worry, your oldest saves will be automatically removed from the cloud (but not from your hard drive) to make space for new ones.
I guess a bug prevented that from happening and stopped registering my saves alltogether.