Coil whine is dependent on the quality of your hardware, not the software you're using. SLI treats your connected cards as a single, more powerful, GPU... so the real question is "Does Unity work with a graphics card?" and the answer is yes... of course it does.
as i understand CW is caused by high fps. in unity editor for simple scene i can see 3000 fps. i wonder if this cause CW.
I have an EVGA GTX 980 and it doesn't have any coil whine. From what I have heard though some cards just happen to have them. If you order one that does I'm sure you could RMA it.
If it's getting 3000 fps, it's putting a lot less effort into that scene than intensive games so I wouldn't worry about it. If you're really worried, just cap it to 60.