The way an actual GBA makes GB(C) games work is due to the GBA containing the hardware for both systems (which is why the Game Boy Micro didn't have GBC compatibility; it lacked the extra hardware). Effectively, it's two seperate systems in one.
GBA-enhanced games supposedly work by checking the hardware state on startup and registering this internally, then uses that to make things work differently. The game cannot and does not make any use of the added hardware; it doesn't have access to anything that isn't already on a GBC.
Hence, emulating GBA-enhanced functionality for a GBC-game would be done in a GBC emulator, not a GBA emulator, and it is there an option for GBA enhancements would need to exist.
While VBA-M, which Mednafen is based on, supports both systems, the core used in the RetroArch appears to only contain the GBA-related code, with Gambatte being used for GB/GBC support (as per SevenSidedDie's comment). The fact that Shantae, a GBC game, will not load on the Mednafen core, indicates that this is indeed true.
I am not aware of any emulators that allow these checks. Most games that perform this check do it to change the color palette to make the graphics look better on a GBA, in order to account for the different screens - but for an emulator, that's not normally something you'd want. You'd have to take that up with the emulator developers, though.
What probably happened to you is a "Bad Egg" has appeared in your pc, causing your game to freeze.
Basically, bad eggs have a chance to appear when you cheat and getting rid of them isn't that easy.
If you want to research more about bad eggs, you can read about them more in this link.
Bad Egg
Here you can see more about how to get rid of them.
Getting Rid of Bad Eggs in Pokémon Emerald
Best Answer
See the developer's page for more info. Quoting from the source:
As Pokemon Light Platinum is a Pokemon Ruby hack, chances are that you are trying to use the wrong codes.