I think highlighting enemy ships on the map based on their strength/weakness to your selected ship would be really useful for finding targets or avoiding enemies. It could have the potential drawback of inducing players to focus too much on micromanaging weapon and armor types, I'm not sure how it would work out. Maybe it should be available but disabled by default, or only show when you press a hotkey (like showing the range of ships in original AI War).
Highlighting on the sidebar I'm not very sure about. I don't think it is of any use at all without map highlighting, but if you have it on the map might as well have it in the sidebar (to make it easy to find the ships there and read the tooltip if you want).
I see two ways it could work though: when you select a ship and when you mouse over the ship type or the control group in the sidebar. Doing it for selected ships would have the advantages that you don't have to keep your mouse anywhere and you don't need to select the ship afterwards (in case you don't want all ships of that type)... however it could get confusing when you have multiple ship types selected. The second option would make it harder to see tooltips for the highlighted types (as you are mousing over one already), but makes more sense as the information is about a ship type and not specific ships/groups and makes it easier to see information about the strengths/weaknesses of AI ships.