Option 2. POW camps are very specialised facilities that have no other purpose. Remember, they need to be able to accommodate different gravities, atmospheres and so on. It's not just a pre-fab huts surrounded by barbed wire.
Transporting POWs also gives hospital ships a second job which is good. And I'm all for adding new diplomacy options regarding them - aliens demanding repatriation, improving relations with them if you hand them over quickly or without being asked, POW camps generating unrest because civilians are uneasy living next door to them, and yeah, chance for escape if the POWs are the same species. Ground units definitely need a chance to surrender too!
But perhaps this all could be a check box in game options like maintenance, jump gates and realistic promotions.