you mean the difference between hermes/waninkoko/d2x?
for games, d2x fix a controller lag issue that rev19 to 21 had. (not totally right, I know)
And added a "IOS reload" blocking method to prevent game reseting/returning to Wii menu, instead of using alternative dols.
Rev17 is working fine, but it's only using a base IOS38, while d2x can let you choose the base IOS.
Base IOS56 as the faster read access from USB.
some games may require a base IOS57 to work, so that's why it's recommended to install the d2x v6 base56 in slot249 (best compatibility/speed), and for specific games only you have the base57 in slot250.
d2x also fixed a lot of NAND emulation problems, but has nothing to do with the game compatibility (unless you want to save on EmuNand)
For zelda, and Like any other old WiiMotion+ game:
You can play with rev17 or rev21. you don't need d2x at all! (but use it if you have it)
Just use alternative dol, watch the video.dol once if you never did, then disabled alternative dol.
The only protection it "could" have is:
Launch the game without any patches (no region or language change/ocarina/etc.), and it will work fine.
The more the loaders are making progress to be noob proof, the more the "advanced users" become noob themselve because they forget they used that method with Metroid
WiiPower made a great topic to explain what's REALLY needed for Zelda, please check it:
http://gbatemp.net/topic/313365-skyward-sword-keeps-resetting-to-the-menu-1st-wm-game-solution/
I'm closing this topic, so you follow the one with the solution.