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How many holes does a donut have?
Now make the donut higher. A lot higher. Now you have a donut-tunnel. Now make the walls thinner. Now shrink it. Now you have a straw.
One hole.
Take a sealed tin can. Punch a hole in it. Punch another hole in it. You now have one hole.
No, but that's two holes. And it's because the holes are not connect by a single, unbroken cylinder. It's the material at the edge of those holes and the 90° turn at the corners that makes the holes disconnected.
The edges and corners mean nothing for the purposes of counting holes. Counting holes is a concept of topology that relies on continuous deformation. All non-opening features of the object just get squished and stretched away in the process of identifying holes.
For the purpose of counting holes a can with two openings punched into it is equivalent to a donut which we know has only one hole.