I finally figured it out.
It appears that the Homebrew Channel does not like certain file names for the folders? So I had to rename pocketsnes_libretro's folder name to something like "pocketsnes" for it to work. But not only that, I didn't know the folder had to have the same name as the .3dsx and .smdh files. So after I did all that renaming, it finally showed up in the Homebrew Channel. I'm not sure why I am the only one that had to rename everything (I don't see anyone else talking about the issue) but it worked. Very strange.
By the way, is it true that the SNES emulators run better when installed a .CIA instead of running them from the Homebrew Channel?
It is definately true. I just downgraded, and installed the emus as CIA and it runs better. Most games you may not notice, but the games that do lag now, will run smoother.