I have a question. Why is everyone so sure it's checking for that extra file?
According to this post http://gbatemp.net/threads/monster-hunter-4-anti-piracy.354640/#post-4773827
Monster hunter comes with 5.1. The extra file was added with 6.X. So checking for that extra file would stop the legit game playing on the firmware it came with.
So why does everyone seem so sure that it's that extra file?
Agreed, people jumped to that conclusion far too quickly. It's way more likely that MH4 simply requires something that's in OFW 5.1 so it naturally doesn't work on OFW 4.5. You would expect that to start happening.
The most obvious fix is for GW to step up their exploit to work on newer FW. (Eventually they'll have to get more fancy than that, once Nintendo patches the DS profile overflow.)