Why are the hidden files/directories seen in Terminal color settings?
If I understand you correctly, this likely has to do with how terminals work. In bash they are hidden by most aliases of ls.

Try ls -a or \ls -a if that isn't working. This is to show all files and escape an alias you might have.

Put simply, the terminal doesn't care about finder preferences because it isn't finder.  

If not, then perhaps terminal simply doesn't respect the finder settings.