I don't really understand -- what is this hole? Is it an air return, that's still functioning, or what? I can't imagine any function that requires a two-foot-square opening, or that could then also be boxed in. Without knowing more, it's hard to give advice.

So ... you would have to give the area, on top of the vent, some clearance. Perhaps your bench/seating idea is best, with lattice around the base. What's happening with the pipe?

You could also build it into the base of a little beverage center, if you don't want to constrain the seating and other uses of this space.

Beverage center might be, depending on the arrangement of your living spaces, a sort of small bar with a drink/wine fridge underneath and some glasses on top, or a place to put a nice coffee maker and some mugs. Or both. Anyway, a thing that could be built against the wall. Just can't imagine you want to keep this thing so far out into the room.

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It reminds me of the vents that used to be in old homes. They were covered with a decorative cast iron grill and essentially became part of the floor. You could put whatever furniture you liked over them because they were flush with the floor. It would not surprise me if similar things were still used in commercial construction.