I think more than anything, the reason why Twilight isn’t upset is because she knows that hibernation only lasts a few months and he’ll be back to normal after that, similar to how in the micro series Twilight didn’t understand why Pinkie was upset about Ponyacci retiring because he would still be there even if he was no longer performing (Granted, Fluttershy would know about hibernation too, but in her case it’s probably feeling sad out of sympathy)