I would not get excited when you let her out, then she thinks that being let out is SO MUCH fun, she may start to act up in the crate, barking, scratching, trying to get out, etc.. & who wouldn't when there's all that excitment when you get let out.

I would treat it just like anything else, if you follow the NILIF rules I would make her obey a command before she exits the crate, if not that just let her out like it is a normal everyday thing. Don't act excited, don;t act dissapointed, just act normal.

Personally I like to leave the crate uncovered if possible, for obvious reasons, there is more air circulation.

And you are on the right track, never ler her out if she is behaving in a manor that is not acceptable.