Most drains are set up so they can be plumbed side-outlet or bottom-outlet. The unused hole is either plugged or used for a hydrostatic relief valve. I have no idea how your pool was plumbed.
A "hydrostatic valve" is a pop-up relief valve that allows water UNDER the pool to flow INTO the pool, when the pool is drained. The purpose is to prevent the pool from floating out of the ground when the ground water level is high -- but they often don't work, and they often do leak. If you don't know what these look like, you probably won't recognize them -- it would just look like that hole was plugged.
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