The purpose of the HM mechanics was to prevent game-breaking situations.
If the original game allowed you to simply delete HM's well crap now you're stuck on an island with no way to get home.
This is increasingly vital when you're actually surfing. LOL IDK HOW TO SURF NOW YOU DROWN.
The game developers did not want customers coming in saying that they have to start over because they forgot an HM.
The solution to this was MOVE DELETER (and in the version of Gold and Silver I believe he is located in BlackThorn City) which was a simple Idea:
give players a place to delete HM's with no possible way to break the game. As i recall Blackthorn City does not require an HM to exit from it, as opposed to CianWood City which is only accessible by surf and fly.
given the fact that Pokemon 3D does have modifiable files, Game Breaking is harder to do.
Keep in mind however that not everyone can successfully navigate their computers files and properly changing values within .dat files, without causing their computers to burst in flames.
So don't make HM's deletable, or else you'll see threads of people wondering why the heck they're stuck in Cianwood.