Does that mean that every single mod must update to 1.6.3, or you loose your nether fortress being a nether fortress, or do 1.6.2 mods work on 1.6.3 like 1.5?
If a mod uses srgnames, doesn't add structures to world and isn't a coremod it will almost certainly not need to even be recompiled. Core mods need recompiling and stuff that adds structures needs to get modified a little bit.
Another crucial thing is after you update with all the mods you apparently need to re-load all the chunks in-game to force-save the structures. If you don't explore your world before updating to 1.7 you'll loose the structures in the non-explored parts. I sure wish that Mojang would at least add a tool to do that offline or an in-game command to load all chunks and not require players to manually explore everything.
ID removal is godsent. Just imagine how much less ID-conflict bugreports there will be.