Use the stud finder on the other side of the wall (the side the tank is on.) Then you don't need to worry about the wood. The stud finder might work through the plywood wall of the bookcase, but it might be kind of dicey. The wall looks to be rather short, though. Odds are there is a stud in the corner and a stud at the outer edge and nothing else.
A hole saw will create a plug (with a hole in the middle.) While you could use it to plug the hole, cosmetically it wouldn't be great. I would use a jig saw with a fine tooth blade and cut a square/rectangular piece out. You can then frame it with ¾" x ⅛" moulding stained to match and put that in the hole. Would still stick out a bit, but not as much.
How much room is there between the wall and your tank? hole saws have a pilot bit in the middle that sticks out ¼~½" At bare minimum you stand a good chance of hitting and scratching/chipping the glass of the tank as you go through. Some bits let you remove the pilot bit, so you could start the hole and then remove the bit. You could still hit the tank with the outer saw part, though. Consider putting a thin sheet of plywood or better yet, sheet metal between the wall and the tank if you go ahead and do this.
All in all, I would either find a different place to put the MP40s or get some different power heads that are internal. Just my 2¢