I havent installed arm9loader yet because personal reasons but shouldnt that negate whatever slowdowns the 3DS may have with higher capacity cards? I dont have arm9loader so I cant speak from experience but its suppose to improve on that.The only reason I won't use more than a 64gb class 10 95mbps read\write speeds is because of the slow down and terrible install times on higher capacity cards.
I had a 200gb class 10 card and it got pulled quick for this reason alone.