If you print each cup carrier in a different color you can easily determine to whom each cup belongs.
Step 1: Print
PLA should be fine since the cups are not so hot.
The recommended fill density is 20% - 25% at 0.3mm layer height.
Step 2: Magnets
I used magnets that are 5mm in diameter and 2.7mm thick.
Insert the magnets in a way that the odd places are populated with the "north" face out and the even places with "south" face out (or vise versa), as you can see at the attached drawing.
Cover each magnet with a small amount of transparent silicon. You can use super-glue or hot-glue if you don't have silicon.
Step 3: Tie the Hooks
Use the thickest thread that you can find that fits into the hole, thin threads are tend to tie together and mess up.
The hooks snaps into the holes and can easily removed by applying a little pressure on them.