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1 'hole' if you can call it that. Imagine if the straw started life as a solid cylinder and you had to bore out the inside to turn it into a straw: if that were the case, you would drill 1 hole all the way through it.
Another analogy is a donut. Would you agree that a donut has just 1 hole? I would say yes. Now stretch that donut vertically untill you have a giant cylinder with a hole in the middle. That's basically now just a straw. The fact you stretched it doesn't increase the number of holes it has.
So as you begin to bore, that is one hole. But when you go through the other side, you have in fact made two holes. I think a donut can actually be thought of either as one hole or two holes, or more correctly; two holes that are the same hole.
Back to the straw; if you make another hole in the side of the straw half way up, would it still have one hole? Or two holes? Or three holes?
A bit like thinking of the human digestive tract, most of us would agree that your mouth is a different hole to your anus, but we agree that they are in two ends of the same system
This would mean a straw has a hole, yes. It would be like a donut indeed - donuts are first whole, then have the hole punched out of them. This meets a dictionary definition of a hole (a perforation). A subtractive process has removed an area, leaving a hole.
But straws aren't manufactured this way, their solid bits are additively formed around the empty area. I personally don't think this meets the definition.
Your topological argument is strong though - both a donut and straw share the same topological feature, but when we use these math abstractions, things can be a bit weird. For instance, a hollow torus (imagine a creme-filled donut that has not yet had its shell penetrated to fill it) has two holes. One might not expect this since it looks like it still only obviously has one, but the "inner torus" consisting of negative space (that represents the hollow) is itself a valid topological hole as well.
On the matter of the doughnut: If you make them at home, you're almost always just rolling a cylinder and then making it a circle. I have never actually punched a hole out of a doughnut. That would mess up the toroidal shape.
But also: So you're saying a straw has 0 holes?
Maybe she's not, but I am. An intact straw has zero holes. If you stick a pin in the side, it has one. If you stick a pin all the way through, it has two.