Any item can be taken out of the tradable items list with a command like this:
Remove automation science packs from the trade list for each planet:
/remove-item-value automation-science-pack
Remove automation science packs from the trade list for Nauvis only:
/remove-item-value automation-science-pack nauvis
That consequently would make it impossible to rank up each item that's removed from all planets. And that can affect some quests that require ranking up 270 items or whatever to red stars, but that quest is in need of being changed to require "all items" instead of "x items" so that it can adapt to such changes.
Regarding the disruption of game balance due to coin loops, this is solved by lowering the "Base Trade Efficiency" setting. Strongboxes on the other hand will be rebalanced in a coming update.