If you cannot log in, like, literallly, just rm -rf ~/.icons/NumixS5* in a TTY and you'll have a working desktop again hopefully. Then try everything again. At the moment I am going to see if I have the latest Xubuntu and test there.
I already got it fixed... My desktop kept flashing, and Whisker Menu and Pulseaudio kept crashing. And I already did that in a TTY.
Something I learned recently while playing with it is you really don't want to be playing with the themes while the appearance properties are opened. An easy way out for anyone else encountering this issue is to just copy everything. If for some reason this issue is encountered again making everything physical copies is the only way out I've seen that doesn't involve keeping the themes deleted outright. So after cd'ing to where the tarball is, these three commands will pull a user out from any downward spiral they encounter while playing with them;
rm -rf ~/.icons/NumixS5_MateriaY*
tar -xzf NumixS5_MateriaY_Pack.tar.gz --wildcards --strip-components=1 -C $HOME/.icons 'common/NumixS5_MateriaY*'
tar -xzf NumixS5_MateriaY_Pack.tar.gz --wildcards --strip-components=2 -C $HOME/.icons '*/*/NumixS5_MateriaY*'
That'll copy everything, and thus, most likely resolve such future issues. The whole symlink thing is more dangerous than I first imagined, and it takes up your available inodes anyway so no use in doing it if you have more than enough space to spare.
As of now I don't have time to try it, but I can later, maybe from a live USB first...
I thought that was a Linux virus - Which is unheard of in my world.
Yeah, what wierds me out is I don't even know how it happens. Like, it's random how that happens. But I assure you, no viruses here unless it's from the Numix PPA. 
I was considering appending onto the archive Git repo an installation script which will use tar as I've shown with variables, maybe when I quit being lazy and get motivated enough I'll make it so anyone can install these themes with only a couple of commands and the execution of items from menus.
I've added an .md file to the repository linked in the OP which means people can just read that for installation assistance. It's kind of incomplete; forgot to provide alternative installation methods but it'll do for now. Tell me if it needs any corrections to the existing material. It also migth have changed since you saw this message depending on when you choose to see it.
Not sure if any of the admins want to do topic cleanup, I'll let them know about my thoughts and we might continue this as a split discussion elsewhere.
Also I replaced the screenshot. Looks p nice.
K, thanks... hopefully people like your theme...
@codic had you ever considered creating a thread highlighting your theme on Gitfoss? I think it would be way better for exposure of your Materia fork. Also, quick recommend; on Codebase, scrap everything there and create an .md file which links to your Gitfoss page.
Codebase... I think you meant CodeBerg XD. I already have a thread on the Manjaro theme, but I'll also make one here on the Ubuntu Mate forum, and probably on the stock Ubuntu forum as well. I won't scrap the contents of the CodeBerg repo for historical purposes, but I will link to the new version and state that this is deprecated.
Codic's icon suite GTK theme has moved, yet again. Hopefully it's permanent this time.
I dont have an iconset, and it will be permanent, trust me. I have a theme - you have the icon set