I don't think there's anything wrong with him taking them out of the box and putting them back Makes sense - lots of toys have that crackly plastic inside them that make the same noise, and they're shiny and something new - fun fun fun!
FWIW my DD1 knows what condoms are and what they're used for, she thinks it's hilarious. She doesn't play with them any more now that she knows what they are, she used to rip the packets open and ask me to 'blow up the balloon' for her... now she sees a box and goes 'Yuck! They're for doodles!' and puts on a pair of my shoes to play with instead