I can go into more detail in a few hours, but essentially it involves hex editing the CIA of the browser/whatever you're wanting to install. It's the same process 3DNUS uses to spoof versions. If you can find the proper spot in the CIA where it keeps its version number, you can change it to 0xFFFF (65535) and Nintendo can't update nag you about them again, because 65535 is the highest version number on the 3DS.
Edit: Obviously, don't install said CIAs to sysNAND without the security of ARM9LoaderHax (I know this thread is about emuNAND, but you know someone will be silly enough to try with sysNAND and not A9LH). I'm not suggesting people make frankenfirmwares without a lot of protection.