Hello.

The shimmer-themes metapackage depends on greybird-gtk-theme and numix-gtk-theme so that they are pulled at the same time.  If you remove that package, there is no longer anything that depends on numix-gtk-theme so it would also be removed with autoremove.

"I don't call that a simple solution for end users." 
Packages are only auto-removed when using the commandline utilities, specifically with "apt-get autoremove".  If you're using these commands, it is unlikely that you're a beginner user.  Since you're in the terminal, if numix-gtk-theme is removed, simply install it back and it will be marked as manually installed.

Marking this one as invalid, the metapackage is working as expected.