Holes don’t have to go through anything.
Correct.
If I was planting a tree I would dig a hole, that had a bottom and sides.
Correct.
Therefore the straw has two holes that just happen to meet in the middle.
Incorrect, you have jumped a step in your logic.
You poke a hole through a piece of paper, you don’t poke opposing holes.
A through hole is one hole.
A glory hole is one hole.
There’s a hole in my bucket.
All singular.