On your points:

First: Yes, that is avoidable through design. It just depends on the foresight of the creators.

Second: Ah, this is an interesting speculation. I'm sure that there would be plenty of controversy around this if airships ever are truly considered. I'd assume they would fly high enough that it would be difficult to actually hit them, though that could be wrong. There's really no guarantee that this wouldn't happen, and I suppose we'd just have to rely on the good nature of people to leave things like this alone. Which, of course, means we're totally out of luck.

Third: I'd assume that there would be "no-blimp" zones near airports or similar takeoff/landing strips. Jets and prop-based aircraft, for the most part, would fly much higher than zeppelins or blimps would. It doesn't make practical sense to fly a blimp that high. This would be another "level" of air traffic, one at a different altitude. They'd share space with helicopter-type craft, which better darn well see a slow-moving mammoth balloon flying toward them.