Only if you try and claim the warranty for something you broke c.f. https://en.wikipedia.org/wiki/Magnuson-Moss_Warranty_Act

It doesn't appear to, however if you ever have to get your machine serviced you have to painstakingly undo and redo the installation, as Apple doesn't guarantee the machine that comes back from the factory will have your extra drive in it.

If I were to do it over again I'd just get a larger SSD and leave the optical drive alone.

Maybe technically, but unless you strip every screw on your way into the machine, they won't know you ever had the cd drive disconnected. Just put it back when you take it in for service.

Not in my experience. I did exactly that (install SSD in cd drive bay, and use orig hd for a second drive), and when I had a fan issue it was not a problem.

Yes, but you can un-void it by plugging your CD drive back in. Note that replacing the hard drive voids the warranty as well.