The downside with .so files is that you can't change them on the fly - requires a server restart (while a qvm can be swapped out mid game and will load the new one on the next map).
q3lcc, I thought, was compiled when you run 'make' - at the very least I never installed it myself anywhere, and it's always been there when make needed it for that step. But it could be that it doesn't compile on x86_64 platforms, I'll admit to my ignorance of the details. Did you make sure to edit the top-level Makefile and tell it to build a QVM?
Pre-posting edit: Damn you kevlarman with your fast fingers. Oh well my post still applies too
