As the author of MultiHack I can say with complete assurance that you can view the contents of a MultiHack file within the program and see/modify any piece of code it may change. There is NOTHING hidden from your view. I did this intentionally as I did not want the program to be used for any malicious purposes.
As for the problem with things as stated that get changed a lot, I have to assume that this is true and MultiHack will not work properly with these types of hacks. Not much I can think of that would change this with the current implementation of MultiHack.