for an object to have only one hole despite both openings connecting through the entire object, we must first determine if the object is either a standalone body (eg. a cube) or a "planar object" (eg. a wall). while neither are without depth, a wall is determined to not be in itself a wholely separate entity -- rather, it is one face to a whole entity, eg. a house, dividing what constitutes the inside of the house from the outside.
making this distinction is important to determine how many holes are in an object that, at first, seems almost entirely comprised of hole, our straw. using this model, we can determine that, being separate from any encompassing object, and not serving as a division between two or more concepts, a straw couldn't be a "planar object," and therefore constitutes having what we'll call "conceptual depth."
to define this theoretical term, "conceptual depth" would be the volume that encompasses the entirety of a concept attributed to a physical object. a straw, even though it is technically a sheet of plastic rolled into a tube, conceptually includes the empty space inside of it. the total volume of the straw, including both the plastic body and the empty space, is our conceptual depth. to compare, a wall, being a planar object forming something else, essentially is an "edge" of that encompassing entity's conceptual depth, and its own conceptual depth doesn't extend beyond its physical body, being that it is the physical body. we can further expand into the idea of nested planar objects, that being several encompassing entities coming together to form a larger encompassing entity, but at the simplicity of a straw, what we currently have established will suffice.
from here, we can surmise that a straw, being a simple standalone body, has an interior, the hollow area "contained" by the plastic. however, as a straw includes the hollow space inside, the plastic body can be called a planar object, dividing the inside of the straw from the outside.
now we can determine how many holes are in the straw, by determining how many openings there are into the inside of the straw. were the entirety of the straw, hypothetically, a planar object attributed to an encompassing standalone body, the hollow interior would be the singular hole. however, the straw is not forming any encompassing entity (we can rule out cups, being that a straw does not conceptually divide the inside of the cup, that would be the body of the cup doing that), and therefore, as its own entity, we can conclude that a straw has two holes.
as an interesting sidenote, the same number of holes exists in the plastic body of the straw, because unlike, say, a house (which has several planar objects assembling the whole entity), a straw is comprised of only one, a single sheet of plastic. both openings in the straw are in this one sheet of plastic; therefore, it, too, has two holes.
conclusion: the concept of a straw has two holes because it has an interior and isn't part of something else. the plastic body that encases that interior, separate from the concept of the straw it forms, also has two holes.