Have never had any issues with Micah...can't speak for him. He's not crated at night anyway. Dante is 9 months and crated, knows he won't get attention for barking/whining in the crate at night. But if he whines/barks in the middle of the night, I know he's gotta go outside. It's rare but happens.
Akira is 7 yrs, and also no house training issues. The other night for the first time in a LONG time, she came over the my side of the bed (she sleeps on the dog bed on SO's side as there is more room there) and bumped my hand repeatedly to wake me up. she NEVER does this. I was half asleep and mumbled to her to go lay back down, but she started pacing and I woke up enough to realize she probably had an upset tummy. Let her out and she did her business, and went back to sleep.
We don't have room for our crates in the bedroom, a 54" wire and extra large furrari. Nor would I want them in there.
Your post is actually exactly why I don't keep them in the bedroom, even if we had the room. Panting, farting, moving around, no thanks.