Freeshop does have a 3dsx, it's the version I useIt would be for the best if homebrew apps switched to valid IDs. Anyone going to miss the Imagine series? Didn't think so.
I don't think there is a .3dsx for Freeshop, but CIAngel should work. Also, as promised, here's a script. I haven't tested it, so backup your NAND just in case something goes wrong. But it should work. I got the information from 3DBrew so it should be right.