If your library is seeming big and gnarly to you, it will probably be really hard to digest for someone who is seeing it for the first time. Creating a refactored hierarchy can go a long way toward helping someone make sense of your code and gives them a nice warm feeling that each component is a encapsulated piece, free of action at a distance in all the other code.

It is true that that the build process becomes a little more complex, but once the makefile/autoconf scripts are written, it becomes simple for the user. Personally, if I see a C lib with an understandable layout and good docs, I'll live with whatever build process that is around. But the simplest build process imaginable won't compensate for a hard to understand library structure.

I think an excellent exampe of this is the Qt library. It has a funky build system, complete with its own moc preprocessor, but the routines are arranged and described so nicely, I can deal with signals, slots, and mocs.