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Fill the metal support beams in with expanding foam.
As for the holes--hobby stores sell mylar sticker sheets in just about every S2000 color. It's super thin and the colors usually match up well (black/silver/yellow/red).
If you don't want to spend hundreds of dollars to have it professionally filled, you can buy some of these upholstery "buttons" from Honda. these are the ones that hold your center console cover onto the console. If you feel along the under side of the edges of the console you'll find them. They are cheap and you just sand them and paint them. Then you trim the pin to fit the hole and silicone glue them on. However, they do stick out. I have a different spoiler to hide them to some degree. I do like "Nobody's" idea about the stickers much better, though.
Let me know if it's the lip spoiler or wing spoiler and if you'd be interested in selling it. I have a New Formula Red '04 and was looking into buying a lip spoiler.
I'm planning to eventually switch my OEM lip spoiler for the Veilside lip spoiler but before I do, I'm going to have my trunk professionally repainted and the holes filled.
if i was still in VA I would fill those holes for you the right way. all these ideas are ghetto. don't sticker or button or bondo them. bite the bullet and get them filled and painted by a professional