Hey Frap sorry for not replying sooner. The Nintendo store does get exclusive merch, usually clothing and random crap - not so much games. Last time I was there I picked up a Gamecube pen and a DS pen/stylus combo (there really wasn't much worth buying at the time).
One of the best items in my opinion were the Nintendo branded Timbuk2 messenger bags. Nintendo actually sells them for $10 less than Timuk2 does (without the Nintendo logo).
Last time I was there they just had a bunch of really bad shirts and jackets. It's been a while since I last stopped in, so who knows what they've got right now. Worth checking out regardless just for the hell of it. After all, how many Nintendo stores are there?
have fun