I agree - all the radalts in helicopters I've flown (including my current type which has EGPWS) see the canopy. It goes without saying that it depends on the canopy density - I'm talking about jungle.
I'm very surprised to hear of 1000 ft calls caused by overflying another aircraft - I'd have thought that a spike like that would be filtered out (again, is for the helicopters I've flown)