If you plumb those bottom holes in the middle of the tank as a closed loop there is no need for check valves. I would think the holes in the bottom of the tank would be useful for a closed loop going to a CO2 reactor if you are planting the tank. Or just put a closed loop for circulation or cap them - if you don't need them you don't need them. That does sound like it could work for water changes too, with a valve and a T attached to a hose between the pump powering the closed loop and the tank you can fill and empty the tank rapidly. Perhaps that is the main reason the holes are there. I haven't done this, emptying sounds fine but filling seems like it wouldn't work through the bottom holes.
The small ones in the overflow would be for sump returns and the large ones for drains. I wonder if the drains are large enough to run as a Herbie? Probably so as planted tanks don't need as much water flow as reef tanks. I ran a single drain for a decade with no clogging issues. I covered and continue to cover it with a prefilter sponge.
Is it going to be a planted tank?
Who gets to go scuba diving to maintain this monster?
What about a big school of corys or hatchetfish as well as discus and smaller schooling fish? Tank is going to be covered, right?