Heh, I doubt any mod would do that, since I'd imagine would require them to switch all the existing normal maps that will come out with the next Media VPs over as well?
Yeah, but with something like WCSaga, BtRL, SoL, TBP, they don't use MediaVP resources for models anyway. They are going to be creating custom content in the first place, so they can do it any way that they like and then adjust the shaders to compensate. I mean, if you made the normal maps also contain height map data, then ALL normal maps would have to contain height map data. The way that it is now, by default, you get to add things as you like, without being forced to do both map types. The big mods don't really have that issue though, and they may want to change things up so that they have less files to deal with. It's mod choice though, but I of the thought that most everyone will just leave it as it is now, since it's probably easier on the artists.
But yeah, I'm happy with it being separate if you don't think it'd be much of a performance issue. 
Nah, the performance impact is negligible at best, at least for rendering. The memory usage impact is certainly there in full force, but I anticipate that most models are just going to go with normal maps and not height maps anyway. The addition of height maps is great for many things, but most of the content people are going to deal with is just small stuff, and 99.9% of the time you aren't really going to get anything out of the height map visually. For things like landscapes, or really large objects, height maps will have a massive boost to visual quality/effect. But using them for fighters and other small objects like that is really just a waste of memory.