Well, I'm subbed to a few mods on Steam while using mods from the Nexus. Let's say I install a texture pack from the Nexus which replaces pretty much everything. Will the mods I've subbed on Steam have zero effect in game?

Don't turn this into a "hurr X is better than Y" thread.

Loose files take precedence over BSA's? That is right, they do!

And they should preferably be avoided, so that you can manage your mods through activating/deactivating esp files, which in turn would activate/deactivate their corresponding bsa files, regardless of the source of your mods.