When the 3DS first came out I can understand the 32 GB limit. However, as the 3DS evolved and upgraded why Nintendo didn't upgrade the 32 GB limit is beyond me. I really think Nintendo should have allowed more space availability in terms of allowing the New 3DS to read larger than 32 GB.
However, formatting your SD card isn't too difficult. I found this link that mentions the 3DS
Fat 32 Format Guide & Program This link is assuming you have a PC and Windows 10. Here's a link if you have a Mac > Fat 32 Mac Format Guide
Also, another thing to note the larger capacity SD cards when properly formatted may take longer for the system to read possibly causing a delay when opening from sleep mode or when turning on. In the event that you need to replace/repair your system for what ever reason Nintendo won't do a system transfer when you send in your old system for replacement/repair. While the process of formatting the SD card won't void your 3DS's warranty; Nintendo apparently won't touch anything exceeding a 32 GB SD card. I know this because I dealt with this very situation myself. I personally have a formatted Fat 32 64 GB SD card in my 3DS right now.