While I'm not advocating splitting things up, it's definitely not up to the file system. The whole stated problem is that some file systems have problems when there are a large number of files in one directory. To be honest, I don't think the 6000+ files we have now is causing problems, but the file system can't internally spread them out, because that would redefine the meaning of a directory.

As for searching, do you do your searches against the actual files on the disk, or using tools based on LDraw? Any change to the folder structure would require updating all tools to support the change, which is why I don't think it will ever (or even should ever) happen. But since the tools would have to be updated anyway, a change in the underlying structure wouldn't change the user experience for people using the tools.