I'm by no means an expert in Unity so I'd like to recommend a little sodium chloride with this reply, but in my experience using 3D graphics for a top-down or side-scrolling (parallax) 2D game is unlikely to affect performance much. In fact, the effect would probably be an improvement. Here's my reasoning:
In any robust game engine or environment, graphics are usually mixed along alpha channels (etc.) during game play -- characters & obstacles layered on a separate background, etc. In 3D, this is complicated with the addition of a Z axis which requires additional depth management including clipping, occlusion, and so on.
At the same time, any 3D engine worth a spit will be efficient, meaning it will not waste too many cycles trying to figure out things like clipping when the graphics blocks are basically just flat planes perpendicular to the Z axis. In effect, the game is simply shifting around postcards on which you probably don't want to apply lighting effects, meaning much of the complexity of a full 3D environment is reduced.
Additionally, 3D engines tend to boast their polygon rendering abilities so you know roughly what kind of performance you're likely to get. And beyond this, 3D engines often make direct use of graphics hardware which can greatly increase both rendering speed and free up the main processor for other functions (handling A.I., collision detection, etc.) 2D engines usually use the main computer/device processor so they can boast greater compatibility, but at the cost of raw power and speed.
In Adobe Flash, for example, we have had robust 2D graphics since pretty much the inception. Many optimizations have been made to the software to make it efficient, and it was pretty darned good until Adobe introduced direct GPU support. As a result, frameworks like Starling popped up that boasted the same capabilities as Flash 2D but with the ability to handle a lot more while simultaneously freeing up the CPU. In other words, Starling is a 2D game engine that uses Flash's newer 3D capabilities, analogous to your question. The answer that Starling provides is quite clear: 2D games can realize significant performance enhancements (plus easier code/effects), by using a 3D engine.
Back to Unity, I'm fairly certain that the same GPU acceleration is used which would lead me to believe that you would be better off using the full 3D engine to create a 2D game; the performance improvements alone would be worth it. Also, as you mentioned, 3D engines tend to have a lot of functionality pre-built -- physics, collisions, etc. It's nice to know how these work but if you're more concerned with actually building the game, these topics are probably best saved until later.
My two cents
Edited by Patrick B, 01 September 2014 - 08:41 AM.