If anyone really wanted to try to lock down a program, try using the prog to appvar conversion that Celtic III has, but only if you're just using it to read just data from these files. The benefit there is that it does not clutter up both the EXEC and EDIT part of the program files menu. I also realize that determined cheaters will figure out how to make the conversion back for themselves (thanks to Calcsys).
I believe the only benefit to locking down programs on the calc is, as already stated, is to keep the program menus uncluttered so people don't have to stare down at potentially hundreds of subprograms for an especially epic game. For anyone trying to learn, I would at least have instructions in the readme as to how to view these files so they, too, can learn from the way you did stuff.
If you went about trying to protect your programs in this fashion, I would suggest doing this as the last thing you do in the project and completely retest the game so that the conversion works. It's suggested to be the last thing done because I wouldn't want frustration coming from trying to look into an overprotected file.
EDIT: tl;dr : Department of Redundancy Department