The Nintendo seal is not a good measure, it seems. The pirates easily duplicate that. Quality is a bit weaker, and it's usually misplaced, but these are things you may not notice until you KNOW what to look for.
I found a helpful post on NeoGAF here. There is one "surefire" method of identifying GBA bootlegs apparently. Underneath the cart, where the prongs are, there is a Nintendo stamping with the cart's code on it. This is one thing bootlegs never appear to duplicate.
I'm not so much worried about the store willfully ripping me off, they sound like an honest business and they've already told me they'd refund me if something was wrong. Problem is, I'm concerned someone ripped THEM off by having them buy a bootleg to resell. However, this copy, although used, comes with a box and instructions... and those are easy to spot if it's a bootleg (look at the back of the box in the link, terrible). So I'm hopeful this could be legit. Kinda hoping this is just someone who had it, got tired of it and sold it to these guys.
Yeah I get the money back, but I kinda want a copy of this game.
Well, I'm in Baltimore and it shipped from Pennsylvania, so it shouldn't be a HUGE wait. When it arrives I'll post images.