I've used clamshell mode for about the past 7 months and I've asked AppleCare about this issue more than once and I always get the same response"
"Mac notebooks are designed to run in clamshell mode without issues...don't worry about it"
When I use Handbrake (or any other CPU intensive program) I DO in fact open the MBP (despite what AppleCare says)...
I've had some fan/heat issues since switching to Lion that have me a bit concerned and I've already had the logic board replaced one my 1 year old MBP...