I think the main thing is that if the bottle has BPA in it, its not good to microwave them - not about killing any nutrients in the milk (which is more typically for breast milk, not formula).

We put a bottle in the fridge with cooled boiled water in it, and leave about 50-70 mls free and then we just boil the kettle. If we boil it before we go to bed, it doesn't take that long to boil again (mind you, we go to bed at like 11.30 or something!) so she's only really waiting about a minute. Then we put in the formula and make it up fresh.

Its awful when they are screaming for their food in the early hours of the morning, DS was an absolute shocker. 10 seconds late and you were in trouble! lol