I read on another site, Apple are able to ascertain if you have jailbroken your device or not, they will simply return your device unrepaired/unrepairable. I understand that unless you can somehow do a Restore on it via iTunes in its defective state, they will not be able to determine the jailbreak. Jailbreaking is done at own risk.
Edit: Found this in a 3rd party website, their disclaimer: "We do not offer any Warranty, or do not take any responsibility for negative results after repair services, if the device has been jail-broken."