The LED doesn't (or at least shouldn't!) stick out beyond the aluminum, so it's pretty well protected. The LED is theoretically subject to damage, but it's pretty unlikely, and I haven't heard reports of problems because of that. I've been carrying Arc AAAs for a couple years now on my keychain and haven't seen as much as a scratch on the LED. A lens lowers the light output a bit (they are never perfectly clear) and would probably be more likely to suffer damage than the LED in the current design. I wouldn't worry about it, though you could check with Peter to see if damage due to that part of the design would be covered under warranty.
- Russ