Thing is CBO handles Unique Units that aren't related to the Civ is by making sure they are a unique unit. The decision-related units aren't a unique unit and were made so since you had a lot of barbarians popping in with decision-related units at the ancient era (Great Galleass at Ancient?! )
Unless telling ShowInPedia to be false makes it disappear. I don't know. I'll have to ask Gazebo about that.
Showinpedia only affects the cipedia - you'd need to edit the techbuttoninclude function to preclude showinpedia units (not sure if I've already done that or not - I may have).
G