it won't be "bottoming out" on the freeway in the lowered setting, since the ride height goes back to normal at 30 mph anyway.
I'm assuming if you have no leaks from the bags themselves, and you have checked the ride height sensor linkage on the wishbone control arms for any looseness, damage, etc, I would also look into your strut mount assembly at the top of the strut, that can make a nasty sound like you are bottomed out. As well, check your sway bar links and thrust arms for wear, if those are worn out they will make nasty clunks going over dips and bumps, I know, because I just replaced mine.
I drove around when i first got my X with 2 blown front air bags, when the fender liners were touching the tire on start up, until the compressor had enough time to fill the bags up. I hit a few bumps and it sounded pretty bad and definitely was bottoming out. You definitely aren't low enough to bottom out unless you have bad strut internals.
My computer isn't letting me post the blow up of the air strut from RealOEM but it looks like the strut/bag is sold as one assembly.
heres a link
http://www.realoem.com/bmw/diagrams/x/y/190.png