I've seen posts that assert that ultrasonic cleaners are hard on aluminum. Does that mean that you shouldn't drop a Parker aerometricl, say a 21 or a 51, with the hood and aero filler into an ultrasonic bath?

Just keep the water/solution from getting into the sac guard. You should be OK. It's not a bad idea to run a 51 through a short cycle in an ultrasonic before you take the hood off (assuming you're going to) to loosed up the dried ink inside. It makes taking the pen apart much easier.