The factory used "well nuts" with stainless bolts that IIRC, match the countersink in the spoiler. You can get the well nuts at really good hardware stores.
These tops are so easy to find, if you aren't in a huge hurry, you might just find one that already had the spoiler on it, and use the new top.
You could try something that went through both pieces of the fiberglass, but I suspect the inner surface isn't flat where they'd protrude.
And yes, in my experience, the spoiler helps a great deal keeping the rear window dry/clean, and keeping exhaust out while the vecicle is moving with the rear window down.