I would guess that when Daniel said “hidden” he didn’t mean what you think he meant.
Normally, computer graphics (including PDFs) are created in the same way as “painting”. You add “ink” which can cover up what is already on the “paper”, but you don’t erase anything.
So in the case of an “open” half note overlapping a “solid” 8th note, the 8th note head is not drawn at all, because the half note on top of it would still leave the black “ink” filling up the half note.
Also, in some music fonts, the “open” and “closed” note heads are not exactly the same shape either, so drawing both of them at “the same position” might create a mess.
On the other hand, two black notes can be drawn on top of each other without any problems, and a marquee selection will select both of them.
Trying to fix this by “painting” the center of the half note white (for example by creating a “multicolored” font using white “ink” as well as black), would be complicated, because staff lines, leger lines, etc., should still be visible in the “hole” in the note head - so you would have to draw the notes before drawing the staff lines, etc., and that might cause other problems.