Question: Do these net version numbers in fact mean that only those with same version can connect to each other?
Yes, this can happen.
This would in fact mean that there will be almost no files on the actual net everytime net number changes, and in fact it`s really bad if that happens any 2 weeks ;-(
Well, this is imho the greatest problem ANts suffers from. Instead of using separate testing and stable networks all ANts releases connect to the same network, and in the worst case this can lead to problems like the one you mentioned above.

I really wonder if Gwren is going to chance this behaviour some day.