Well yes & no. I'd make an educated decision based on what had gone wrong. If the screen was broken for example I'd say that wasn't the optibay - but then again if the connectors to the DVD drive (where the optibay plugs in) appeared damaged I'd take it on the chin and pay for it myself.
On the AppleCare front - I never buy AppleCare as my laptop is renewed every year anyway, I rarely go beyond the 1 year warranty.
Essentially if you make changes to your machine that breaks the warranty you have to take the risk that you can't get something repaired under warranty don't you?
I accept that risk personally, as I think it's forth it for the flexibility I gain from the configuration. Others may of course think the risk is too great.
It would be pretty impossible to tell if you'd put an optibay in, taken it out again and put the DVD drive back in. The MCE OptiBay only has a single screw securing it whereas the SuperDrive has 3, so you need to make sure you keep the screws.
Like I say, it's an educated risk.