saving out iff's should be the fastest .. all other formats are converted from this to tif or jpg etc after the frame is completed
I suppose it's possible that if your file server was slow larger uncompressed files would take longer to write
you can render out just alpha from the render settings..
I will mention that the jpg settings maya uses are horrible and it would be better quality wise to make jpgs from another program if you have to do that.. if you are doing just because of file space it seems kind of ridiculous considering how cheap drives are these days