Bad mouse smell is just mice being the dirty little stinkers they are. Ammonia on the other hand is from urine sitting and building up which in turn means they in need of cleaning.
Mice stink is pretty rough, its hard to keep the odour down. Mice4You has a product they use for their mice to help. I believe they are selling it at $4 a bag???? Alot of people use vanilla in their water as well. I have used vanilla in the past but it still stunk pretty bad so now I jsut try and bare the stench as well as I can...lol

If it isn't in need of cleaning, then the dont clean the cage simply becasue of mouse smell, it will only make it worse. The males will scent the cage even more because their odour keeps disappearing.......