You can plug them with a small screw/nail and some silicone. Make sure that they are bigger than the opening so they dont fall in it. Thats what I did.
You can remove them if you like,(assuming your smog pump is gone) just make sure they are capped off really good. Like stated above, use a large bolt, or screw. You can buy plugs at most local parts stores for a few bucks. Just make sure they are sealed, or you will have a vacuum leak. You don't want that.