Their survival will depend on how deep is the pond. If you only get a few inches of ice on the top but the bottom don't freeze, they will be just fine. Their metabolism slows down as the temperature goes down. You took them out and they are fairly warm now, so be very careful bringing them back out if that is what you choose to do. No need to let ammonia out, since they will not be producing much once their metabolism is slower. If the bottom of the pond freezes, it may be harder to get them back in the spring. It all depends for how long they are frozen. Making the decision to keep them indoors for the winter is a big commitment. You will need to make sure they have a good filter. Kois can produce a lot of waste in a short period of time. Once they are back in room temperature water their metabolism goes back to normal and they need to be fed.
When I lived in Plattsburgh I had a very large basement with a few 80 gallon fish tanks. The temps up there are so low that most ponds freeze to the bottom. for about 5 years I housed the kois from my friends ponds during the winter. My Dr didn't know how to take care of his fish and after loosing his kois he asked me to care for his new ones. In the spring I would bring them all back. I wish I had the space now. I love tanks.