The way I try to handle situations like that is: once someone has the item or has fully interacted with something in a way that they don't need access to it anymore, I'll use the STOP variable to prevent them from clicking it, to save them some clicks if there's already plenty of other things to do or explore. However I may also check the "Visible When Inactive" option, which will show the action link (such as "Open the trunk") but have it grayed out and non-clickable.
If you're feeling ambitious and it makes sense for the flow of the storygame, you could even connect some on-page text that says something like "You already got X item from the trunk", in addition to graying out the link or making it disappear.
That method mainly reminds the reader of what they've already accessed and obtained. Let's say you had a room with a dresser, a desk, a nightstand, a closet, and such with over a dozen different things to open. This combined with other rooms in a house, with their own objects to interact with. The reader can easily get disoriented if you have them randomly exploring too wide of an area for that one pesky thing they accidentally missed to progress forward. That could leave them backtracking and going in circles until they find it, which probably isn't enjoyable for some people. Using that house example, if you gray out any object they accessed (that was empty), and any drawer they got the item out of (but only after they grab the item), it'll help them navigate things better and easily know if they missed checking a spot or not. It does drop the difficulty though, so that's more of a design choice that could go either way. You can also combine the methods, and keep some things accessible, while removing access to others.
Personally speaking, if you have a lot of different locations to explore and the reader may have to backtrack in case they missed something, then either removing the trunk link or graying it out (as described above) would improve the quality-of-life. Just make sure to not accidentally remove access to something they may need to go back to. In general I wouldn't mind you doing what you described.