Apparently he can heal from wounds instantly, according to [url=http://www.comicvine.com/superboy-prime/4005-40756/]comicvine[/url], though to what extent I'm not sure. And even while holding his breath he can zoom into the nanites and burn them out of the air with his heat vision. 

Regardless your solution, while imaginative, is extremely deliberating to just about 90% of fictional characters. Superman; nanite bomb to the lungs. Batman; nanite bomb to the lungs. Harry Potter; nanite bomb to the lungs. Goku; nanite bomb to the lungs. There would be survivors, but there wouldn't be many.