SDHC means 4GB to 32GB. The old SD standard only goes up to 2GB. SDXC is the newest standard, going up from 64GB onwards until they hit another wall with the technology.
Sky3DS can handle the latest SDXC standard, so it should be fine with anything up to 128GB so far (although it seems to have issues with SD cards, 2GB and below). It seems odd that it would be considered an issue.