Why not? I have put in a 32GB card for a test. No problem.
It should also work if you format it to FAT32 - like wormdood already said. But... do you really need more than 32GB for DS games? Many games are small, about 64MB. Okay, some like Pokemon white/black 1/2 are fairly big.
If you want me to test SDXC, just tell. If you like I will prepare a 128GB card (will take some time) and play this evening with that and see if it works stable (with R4i Gold 3DS without Plus, but it should make no difference).
Is 2x 16 GB[1 for the for the R4I Gold Plus and my CFW for 3DS games] enough?
And could you test this SD micro card? https://www.dataio.nl/32gb-micro-sd...asYeNHdWaXZiTzXg4KMQZ_7sa26MJ4oAaArE6EALw_wcB
SANDISK 32GB MICRO SD ULTRA UHS-I 80MB/S