Okay:
On one side, we have your friend who claims that his 64GB SD card would not work on his 3DS. You also have Nintendo's official site which states there is a limit of 32GB.
Only thing which I find odd is that there is no additional info for your friend's 64GB SD card. For all I know it could have been a fake or not properly formatted.
Nintendo's claims about this limit come from the fact that the SD Association's guidelines (Which is supported by their commercial formatting tool) do not allow SD cards formatted in FAT32 cannot be larger than 32GB. What this means is that you cannot have a single FAT32 partition on an SD card that is larger than 32GB.
What I propose is that those claims are artificial limits. What I fall back on to prove this point are various forum threads, news posts and maybe videos.
First of all, what seems to be the case is that there have been claims by various users all around who claim they have successfully loaded an SD card larger than 32GB on their 3DS.
If it is indeed true, then that must mean that they achieved having a primary FAT32 partition larger than 32GB on a single SD card. It is fact that 3DS will not recognize any other file system other than FAT32.
What we have to backup such claims are the following:
Code:
http://lofi-gaming.org.uk/blog/2013/10/25/updated-how-to-upgrade-your-3ds-sd-card-to-64gb-and-beyond/
http://www.gonintendo.com/s/184255-using-a-128gb-sd-card-in-your-3ds
https://www.youtube.com/watch?x-yt-ts=1422579428
http://gaming.stackexchange.com/questions/133045/what-are-the-specs-for-the-highest-end-sd-card-the-3ds-can-support
Therefore, I can conclude that the 3DS can support SD cards larger than 32GB, even way back to 4.5
The usual argument is that these sites have no authority. Yes, that is indeed fact and I have nothing to say against that.
What I find wrong with such logic though is that such logic is flawed, in that this is what we do all the time (We are at GBAtemp hacking our 3DSes). We are not following the authorities' guidelines, we are doing something that is not intended.
Formatting an SDXC card to FAT32 is unintended, and you are against that.
Why then are you not against hacking a 3DS?