The simple answer here is that computers are stupid, and that the computer can't read your mind.
Most "Hole Correction" algorithms tend to go with a simpler geometry rather than try to create a more complex one.
Rather than use your complex example, let me try to explain using a simpler item:
Here on the left, you can see that there are two holes (top/bottom), but there is no internal structure.
If you use most any "Hole Correction" tool, it is going to just plug the two holes as surface defects, and not create a passage THRU the object.
What is necessary is to have the vertexes that I've outlined on the right in white, and you must have the faces shown in yellow.
Your model is missing these "internal" faces.
To repair this, you must do one of two things:
1) repeat the original subtraction, ensuring that interior faces are created properly.
2) if your tool allows, you could add the vertexes and faces manually