I've been adding in the lists from the Chinese Link textbook and have been removing some of the supplementary vocab from my study list (for example, I doubt "wife of elder male cousin with the same surname" is an important one for me to know off the top of my head. However, when I remove them from study, they're still on the list with no indication that they've been removed from my study queue.

Could we get something where these removed words show up in grey or something, so we can have visual confirmation that certain words won't appear?

The boxes on the right of the word list shows you which parts you are studying and which ones you aren't based on the colors. As long as they're white and not bold, then you're not studying them (click the link above those columns for a more detailed explanation).

It sounds like though you may be trying to remove the words before they've been added? The system gradually goes through the list and adds everything from every section you have enabled. You can only remove words from your studies once they've been added in this process, though. You can either delete them from the list page or the practice page when they come up.