Sorry, still working on getting the hang of quote boxes, etc.!
To my dismay, I haven't seen any pics of AE with earrings. Have you had any luck, Stacy? 
The way you describe the possible reason for the hole diameter difference is exactly what I thought, too. It's consistent with the little research on handmade beads I've seen.
Here's to computer screens and magnifying glasses!
No luck with any earrings... the earrings back then would have been the old-style 'clip-on' as pierced ears weren't an 'American' thing until the late 50s. Not saying Amelia wouldn't have done such a thing anyway

but for now, I haven't seen any sign of her wearing earrings with her flying outfits.
If the bead is Amelia's then I would go with it coming from a bracelet, necklace, or some other ornamentation (a button, a bead from a shirt, an ornament on her knife or an ornament from some unknown gift).
She wasn't wearing a bracelet in her last photo, but she was wearing a watch. Again, no sign of earrings, though.
A bead like that seems more likely to come from a woman rather than a man, but as Jeff pointed out they were also used for fishing.
I also thought about what the Coast Guard (who were stationed on Niku) might be doing with such a bead. That gets into all sorts of scenarios such as a guy keeping a string of beads as a memento of his gal, or any number of other situations.
Please update if you find anything

And I'll keep looking too...