That's called desync (you didn't have a weapon in hand or ghost bullets) and bullet penetration is a thing in DayZ.

Happens to me infrequently as well have to restart the game and usually works after that sometimes requires 2 restarts.

Believe the new wrench is required to remove parts, I've also been unable to remove car parts but haven't found the wrench to test it so I could be wrong.

Switch servers then you'll be unstuck

I have no problem surviving just like many others, DayZ has a very steep learning curve and is a video game so 1-1 realism isn't possible nor would it be fun.

Do you have some sort of glasses on when trying to use NVGs?