Like I said earlier in the thread that theory makes no sense because Emmett and Howard built the bunker together. Howard knew the air filter room was there and since all of the stuff with his daughter happened before the attack, there was no reason he couldn't have entered it from the outside as opposed to the air vent. There's no way it would have been his own daughter that would have been hidden there.
It doesn't matter if they built the bunker together or not. The room only had two exits: the way that led outside and the ventilation shaft. Now considering it was locked from the inside, it means that Emmet was the only one who could have left the room after it was locked. This had to have been a collaborative design between both parties though as a means to prevent anyone from the outside from getting into the room. But regardless of, it also means that Emmet could have kept anything or anyone in there without Howard's knowledge since he would be the only person with access to the room after it was locked.
For a different theory I just thought of while typing that, what if Howard's reasoning behind kidnapping Michelle was because of the air filtration room? He sees her at the gas station, on his way back the attack happens and he realizes he has no access to the room so he drives her off the road to abduct her as a contingency should he ever have need for someone to get into the room. He himself can't get in, so someone has to right? He wasn't expecting Emmet (he fought his way in, remember?) so he had to think fast and she was his best option at that moment.
Oh and Howard showing up clean shaven with ice cream after he killed Emmet? I think it was meant to be a type of "celebratory" moment. The person he suspected of allegedly having killed his daughter is now dead, which puts him in a cheerful and sane peace of mind. Which is clearly short lived when he feels betrayed by seeing Michelle's plans for escape.
EDIT: Well he does say in the movie that his daughter's mother turned her against him and they left and went to Chicago. Though the movie does hint that his daughter was actually killed (assuming the girl in the picture was Megan, which I believe to be true).