One point that never seems to be mentioned or considered is the relative fragility of the vertical standpipes used in bottom-drilled tanks. You have a plastic pipe the height of your tank, screwed (or I suppose possibly glued) into a bulkhead on the bottom but otherwise unsupported. The amount of leverage that can be applied from having the top of that pipe suffering an accidental elbow strike, the careless use of a tool or net, or even the unwelcome attentions of a large and determined cichlid or other fish, can result in breakage right at the bottom. If you're there when it happens, it's a mess; if you're not, it's a HUGE mess.
Having the standpipe surrounded and partially protected by another larger pipe or column mitigates this, but at the cost of being much bulkier and uglier.
After one such mishap, caused by a mid-sized turtle jamming himself between the top of the standpipe and the tank wall and then pushing with all his might, I have never used bottom drilling again, except in those cases where I have installed one for the sole purpose of complete or partial draining. In that case I will put a valve on the outside of the bulkhead, and also cap off the inside with a simple threaded cap which must be removed to drain any water; I like redundancy. Nothing sticks out waiting to be smashed or broken.
For me, side-drilled near the top is the only way to go. Less likely to be whacked in the first place, and much more resistant to damage in case it is somehow struck.