Why doesn’t shrunken stuff still weigh the same?
Wow that is a clusterbomb of a physics question. Its been a long time since I did physics but basically the guy was able to change certain constants within an atomic structure and make them, well, non-constant and subject to change. And thus those rules are broken / re-written by him, stuff shrinks or grows.
But, even though shrunk, stuff SHOULD have the same weight. After all it still has the same number of atoms, however, if this clown was ALSO affecting the coupling of particles of matter with the Higgs field, then theoretically you could make the mass of the object, lighter, or heavier. So he was both affecting the coupling of matter AND made the constants of atomic structure variable.
Why can their shrunken bodies still metabolize the normal sized oxygen molecules? How can they still eat and drink normal sized stuff?
You'd need a biochemist to answer that one. Odd really as all the receptors for oxygen on their cells would have changed size, should they have suffocated?
Why does getting zapped with the shrink ray a second time make them normal size instead of making them even smaller?
That one is just purely plot reasons IMO.
How did they know exactly what spot on Harry’s body the villain would aim for?
Logically the chest is the best bet, its the largest and most convenient area to hit on a human body that is facing you.
You are correct, shooting at the chest is easier then going for headshots.
As to the rest of the questions: chalk it up to the same comic book magic that:
1. Allows most people to not realize Clark is Superman even though it's blindingly obvious
2. Keeps Flash from starving in an instant due to his hyper metabolism
3. Enables Batman to cheat death on a regular basis
4. Enables Punisher to cheat death on a regular basis
5. Enables Banner's pants to stay on when he becomes the HULK