Nope, NGUI doesn't handle this itself, neither does Unity for that matter.
If you're getting to those sizes, you really gotta ask yourself if there are sprites in there, that should rather be textures. Anything over 300x300 might as well just be there own texture. Alternatively, you can start segmenting your atlas into smaller atlases in logical chunks, so all sprites for a certain screen or set of screens are in the same atlas etc.