Ah ha adolescent piggies. Yes you can expect a little more dominance challenges and stink as the teenage hormones are raging. It will pass in time
Have you tried getting an air purifier? I've got this one permanently set up in my room where my three girls are. They're on hemp bedding and I fully clean the cage once a week. Whilst you can still smell the hay, they don't smell bad. Maybe it will help?