You've explained nothing actually. You keep reverting to penguins but the penguins habitat offers valid reasons for their flightlessness. A cormorant in the Galapagos is a whole other basket of fish.
There may be a valid explanation of why those cormorants selected flightlessness but you sure the heck didn't offer one. Cormorants use their legs to swim.
Well, I could cheat and ask my brother, but I won't, and will just guess based on absolutely no knowledge whatsoever. Flight uses up a lot of energy, and if it is not needed for survival (from predators and for food), then dumping the capacity to fly might be a survival advantage because the temptation to use the wing toys that waste energy might be too much. If it is there, the birds will use it.
Just a guess. How does it "fly" as it were? :)