Not at all. The only bad thing happens when you drop both a folder tree full of song files, *and* some playlist files contained within those folders, onto emplode. Once upon a time, that would cause each song to be installed onto the player twice, thus wasting disk space.

I'm not sure if it still does that in 2.0. Even if it doesn't, even if it duplicate-checks in 2.0 and discards the duplicates, at the worst then you're making the import take twice as long as it needs to take.