Get the holes filled and painted is the best option. Or if you are on the fence, you can get some rubber plugs for the trunk holes. That's what I did on my '01 GT, since I had the spoiler on and off quite a bit lol.
The rubber plugs work great in case you change your mind... or you can junk yard an extra deck lid. Hopefully the paint under the wing will still match fairly well. IMO these cars look good with no or the termi spoilers.
FWIW mine had a stress crack in the sheetmetal under the wing when I pulled it off