According to this (Unity 2D vs 3D), Unity 2D is always faster than 3D. I know the comparison is for Unity 4.3 but it is probably still relevant for Unity 5.
The above comparison is not an official benchmark done by Unity, so take it with a grain of salt? Probably the best way to be sure is to do the benchmark oneself...
Here is an excerpt from the blog:
So if you are developing 2D games today, there is no excuse for starting to use the new Physics engine. You’ll get better performance, meaning you’ll have more CPU time at your disposal to create even better games.
It is their word, not mine though.