With the frequent release of new RC's, I think most of us just reflash and reinstall and that cleans up all of our dependencies.
Some of us have a Windows background, and so we are used to formatting our machine regulary to clean them up.
Seriously, though, maybe when pdaXrom comes to another stable release, this will be a bigger issue to more people.
As it is, I find that the package manager in pdaXrom already works much better than the one in SharpROM (and clones). I can even use the GUI with confidence. The GUI package install in SharpROM was evil in my opinion. Maybe it was just the lack of any visible output though.