Unlike your phone, the 3DS doesn't seem to make use of faster read/write speeds.
Using a sandisk 64GB SDXC in mine currently, got a wicked deal, but to be honest I would have rather bought the cheaper variant as I see no difference in the speeds of the crappy SD card that came with my 3ds and this one.
Only trick is the card needs to be formatted to fat32 from exfat. I believe fat32format.exe entered into google yields an easy app to format your card. In addition a 64GB card gives you around 480000 blocks.
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