Pardon my likely ridiculously obvious, easy-to-answer question.
I don't use the launcher, I don't like how it installs things in silly places. I'm installing them with 3Viewer instead.

The package files that come from most sims3pack files (objects, clothing, etc.) all have long strings for names rather than, say, aftopllama. In TS2 we could rename those files and all was fine... can we still rename them in TS3, or do those filenames actually serve a purpose?

Can I get all neatfreak on my package files or will it bork the game?

I'm...not sure. Have you tried renaming a file to see if it works? (make sure you keep a backup of the original file).