definate answer is... no you don't have to remove them. The covers drop right over them. However... on the left side, you might have an issue with the cover clearing the brake booster while the plugs are installed. Play it by "ear" on the left side.
What's the big deal with pulling the plugs anyway? You've already got all the work done by pulling the coil covers and the coils. Then you can get a look at the plugs for plug wear and the associated issues with different types of wear; it's like checking pulse, heart-rate, blood pressure and all that other fun stuff... gives you an idea on how healthy your engine is!
Be sure you blow the plug holes out with compressed air before you take the covers off... keep all that :q:q:q:q from running into your engine.