I wouldn't worry. My boys both just have one nappy over night and they are both pretty stinky when they wake up. If i'm a bit lazy and forget to put DS's nappy in the bin his room reeks (not that i leave stinky nappies around his room...but you know what its like)
I think its just all the wees building up over night and the smell becomes really concentrated especially in disposables as i guess they don't 'breathe' so it keeps all the stank in