Generally, the Apple Store employees won't care if it's jailbroken if it's a hardware issue. The legalese clearly states that it voids the warranty, but they don't care, and probably jailbroke their iPhone too.
There's two issues here, though. First, if the SIM tray was broken, it was probably done by you. That's "accidental damage" and they won't fix it. It's similar to dropping your phone and shattering the screen then asking them to replace it. Of course, the part costs probably $0.01, so they may fix it.
Your serial number is printed on the tray, so if you buy a new tray, the hardware display of the serial number will be lost. This is less of an issue though because it's still accessible through software, and if it really comes down to it, the serial number is printed on the phone's logic board, but most Geniuses don't know that.
