Should you Megger test transformers?
You have my upvote, because I am often testing motors, but never had a neat specification where the lower limit of resistance is. You can megger as much you want if you are below the specifications. 

If I remember from my university days, the test consists of applying a single pulse at 1.4 x max rated voltage and you may never repeat the test again, short answer. Well it is more complicated like that: they start at lower voltages, calibrating instruments, then rising voltage 3 pulses, finally one single pulse.

For test purposes you actually measure the insulation at lower voltages than max. declared.