Yeah, logias don't regenerate when hit by a weakness of their element type. Like when Robin tried to get Crocodile wet so she could stab him, for example. Getting hit by haki is kind of strange. Presumably Whitebeard used a haki stab on Aoukiji, yet it didn't hurt him (my guess is Aoukiji purposely opened up a hole in his chest?), however, I think Akainu looking all sliced up by the commanders was filler content, though...