I don't think it's that much of a problem with Stack Overflow (although it's possible), but it's slightly more problematic with Server Fault and even more so with Super User. As new Stack Exchanges with similar topics open up, will they be linked to in the FAQ to ensure users can get to where they need to be to ask their questions in an appropriate venue? And will the definitions of the three trilogy sites change over time to make things that were once on-topic off-topic in favor of moving some content off to a different exchange?
One of the reasons for the existence of the new SE 2.0 sites is that there are questions that are currently off-topic for SO/SU/SF that people insist on asking.
I think that all that will happen is that the existing site boundaries will be more rigorously enforced. There will be complaints, "but question X was allowed", but all that will do is cause question X to be migrated to the appropriate site.
Yes. When I loaded up SO for the first time this morning, this question was at the top of the list: Game programming
It's just a request for info/tutorials/suggestions on how to switch over from "general programming" to game development. The OP was immediately advised in answers and comments that we now have http://gamedev.stackexchange.com.
I'm sure they'll have to keep revising the FAQ for all the computer related sites to keep things up-to-date.
I think that a site with a strong simple identity like SO will be reasonably safe. One with a more complicated identity (see the SU FAQ - on topic means this, except for this list) is more likely to have problems.