The safest way to do it would be to put a bulkhead in the hole, and have a standpipe extending from the bulkhead to above the water line. Then you can cap both end of the standpipe/bulkhead for double insurance against leak. <Or you can run your canister plumbing right in the pipe.> That of course means you would have a pipe visible in the tank.
You can cap the bulkhead under water, eliminating the pipe, and hiding everything under the substrate .... but if your cap leaks, your tank water is on the floor!
Finally, you can silicone a piece of glass over the hole. this is prob the least safe method, unless you do it properly. If I were to do it, I would use a piece of glass that runs from one edge of the tank to the other (front to back is usually the way to go, but you can go 4' side to side ...), and 6" pass the hole.
I would use a good thickness .... 1/4" may be adequate, but I'll prob go 3/8" to be safe. You will have to reseam the whole tank if you do this, as it would be risky to attach new silicone to old <Same advice regarding repairing just one section of a seam ... You should do the entire seam, as new silicone don't stick well to old.> ... My suggestion is prob overkill, as some people just use a small piece of glass over the hole .... but you have to sleep at night.
The edge to edge glass patch is a standard way of repair a cracked tank bottom. (From what I read, never have to do it ... I got rid of my crack by cutting the cracked part out & making a smaller tank...). Reason for the big patch is that the patch is bonded to the vertical panes of the tank, and you are not depending on support from the bottom pane which might be weakened by a crack (or the hole.)
80 gal FW with 30 gal DIY wet/dry/sump.
9 fancy golds, 1 hillstream loaches, 1 rubber-lip pleco (C. thomasi), 3 SAEs, small school of white cloud minnows, planted.