Low profit didn't stop twelve (after the 2nd movie) The Land Before Time sequels, Jurassic World, Surf's Up 2, and others. There could easily be a third Happy Feet movie. If Surf's Up, the less popular of the two, got a sequel after ten years, then Happy Feet can easily get a second sequel; reception to the sequel has warmed up in recent years anyway.
Edit: That would be an issue, though, as to who would take Robin William's place as Roman and Lovelace. I can't think of anyone that even sounds remotely close to Robin Williams right off the bat. Maybe Danny Trejo could do it, but I'm not sure; if not, then Dan Castellaneta, because all these years I thought it was Robin Williams and not Dan Castellaneta who voiced Ramon in the video games.