Neither freezing nor cooking will significantly effect the protein content of the mixture.
Denaturing the protein is not going to cause it to have biological value of zero. Sure, it stops the biological function (which just means that it loses the 'extra' benefits such as immune stimulation, anti-cancer etc etc) but the digestion and absorption of the protein into the body is basically unaffected, so you still get the amino acids/protein.
The issues are worse for the more 'refined' powders (so hydrolyzed is more easily damaged than isolate and your concentrates are more robust again).... But even so - the degree would not be significant.
I wouldn't rely on it for your PWO meal, but at other times of the day it should be fine.