......
Theoretically, there is nothing wrong with that idea. Any more than there is anything wrong with wanting nVidia to release a multilayer DDS format so that each frame can be a layer in a single image. Or anything wrong with being able to have a container file that can stuff DDS files together the same way ANIBuilder stuffs PCX files together to create ANI's. Or hell, even to just read them out of store-only zip files.
FSU wise, it so far has not been very messy except in trying to find out what ships share what textures so that you don't end up with unintended effects. I personally would shudder at having to sort them all out into sub-dirs, but I can admit that it does have a certain aesthetic....I just wouldn't want to be the person writting the cfile parsing commands for that.