They have been gutted, but are whole otherwise.
You can cook with the gills on, that is to say they are not harmful. However, it is very difficult to remove all the scales if they are left intact. Same reason that the fins are trimmed.
I've baked whole tilapia quiet a few times and I always remove the gills. They are not harmful like chef Lisa said but they do have some gunk in them sometimes and that could be unappetizing.