Never heard of a Sport coming without a hood. That was a part of the whole 'Sports' package. Rear spoiler would've been optional. Besides what the badging actually says you can identify a Sport quickly this way...
Limited will be loaded... Leather, power everything, more than likely have nav, etc.
SR5 will have 16" wheels, black mirrors, chrome door handles, chrome tailgate garnish
Sport will be like an SR5 interior with color differences. Mirrors will be painted, tail garnish painted
The SR5 for '05 had optional 17" wheels that were the same design as the Limited that year. In my area, just about every SR5 on the road has those optional 17" wheels. I don't think I've ever seen the 16" wheels on a 4th gen 4Runner other than in pictures on this forum. You are correct about the black (unpainted) mirrors on the SR5. The Sport Edition and Limited came with body-color (painted) mirrors. The SR5 for '05 did not come with chrome door handles or tailgate garnish.
To the original poster: Here's a sure-fire way to tell if you're looking at a Sport Edition or SR5. Check for the XREAS shocks. They have a hydraulic line going to them. XREAS was standard on the Sport and not available on the SR5 (and optional on the Limited, but I don't think you're looking at a Limited). It is possible that the XREAS shocks were removed, but you should still be able to see the hydraulic plumbing or if it was ever there in the first place.
The mirrors are another good indicator. Sport Editions and Limiteds came with body colored mirrors. SR5 had black plastic mirrors.
Sport Editions also came with silver painted center sections on the lower front and rear bumpers. The SR5 and Limited did not.
You can also check the wheels. All regular Sport Editions came with the same style 17" wheels from '03 through '09.
Another good way to tell is the seats. Sport Editions only come with cloth and I'm 99% sure that the cloth seat style in the Sport Edition was only available on the Sport Edition. Most Limiteds (if not all) will have leather, and the cloth in the SR5 was different than the cloth in the Sport Edition.
Of course many of these things could have been changed by the prior owner(s), so you might have to look at a few different things to determine if it's actually a Sport Edition or not. But the hoodscoop should be there for sure, no doubt about it.
EDIT: One other thing I forgot. The '05 Sport Edition had silver painted roof rack. The SR5 and the Limited had black roof racks.