Many manufacturers are willing to overlook such things as long as you mount the stock cooler back before sending the card for repairs. It's never certain, though and depends on the service you're sending the card to. Officialy, tampering with either hardware or software voids the warranty.
The biggest issue with swapping a heatsink is the possibility of doing physical damage to the card which is sure to void the warranty. That's also the main reason why companies don't allow it ( officialy, that is ).