On the one hand, for a price difference of $2, I would go for the version with the plastic cover.

On the other hand, with an external webcam, I can simply disconnect it. If you have a laptop built into a laptop that is not so easy to do. At least, you have to trust the laptop's manufacturer to do that, while a builtin plastic cover is so simple one does need to "trust" it; at the same time, you can't retrofit it on a laptop... :(