I would definitely keep the bulkheads in and just plug them if they are threaded. If they aren't threaded I would pick up a couple that are, and then do likewise. Those holes are going to be far more structurally sound with those bulkheads in them.
Oh, and if for some reason you do just cover it with glass, make sure the glass covers are on the inside of the tank. I don't mean to insult your intelligence if that seems like common sense to you, but it's much preferable to the weight of the water in the tank blowing the silicone seams open all over your floor if you happened to overlook it, lol.