Yes freezing Chilies does make the chilies hotter.
Whenever I've frozen chilies the chilies have always gotten hotter and hotter the longer they stayed in the freezer.
The freezer will extend the life of the chilies but just beware that when you remove them from the freezer that they will be much hotter than they would be if they were not frozen.
Still though hotter chilies are great to eat and I love them much hotter because I love hot and spicy foods.
The hotter and hotter the chilies are the much better flavor the food has when using the chilies in them.
Encyclopedia of Country Living says to remove any chillies before freezing any food containing them or the chilies do get hotter.