Is it safe/sanitary to run your toilet drain pipe in a 2nd floor apartment through the existing kitchen (pantry-style) cabinets? The pipe would be open and visible with the cabinet doors open. Is this OK?

Hi New and welcome to The Plumbing Page at AskMeHelpDesk.com
As long as the drain isn't leaking I can see no health issues, Good luck, Tom

Plumbing lines are run through walls and chases all the time. You may want to insulate and shield the piping just to reduce noise in the cabinets.