I drilled the bottom of my tank and used it for closed loop. If thats what you want to do, then it should be no problem if done properly. It looks like that tank was drilled for one drain and two returns. you can use Sch80 heavy duty bulkheads and put good quality union valves and you are good to go. you can hide the returns and drain by surrounding them with rocks for a clean look.
If you want to close them up permanently, you can get a piece of acrylic (1/2" or 3/4") and bind it to the bottom of the tank from inside using weldon16.
That stuff chemically welds the pieces together right?