No the card class makes nearly no difference. You won't see huge differences between the preinstalled class4 card and a class10. I won't go into much detail but it has something to do with the 3ds' cpu and the encryption.
Theoratically you can use >256gb cards. But the sdio chip from the 3ds has bugs with cards >32gb. They will boot slower than normal.
The 64gb card need over 13secs to boot sysnand. And bigger cards will be even slower.
I recommend max 64gb to get a compromise between speed and size. Keep in mind there is also a limit of how many games you can install (about 300). many ppl use 128gb too. So do what you want
Actually it does Larger cards have better Sequential Read/Write Speeds which is good since the Emunand/Sysnand is constantly accessing the cards.
Also card life wise Larger Cards are better Due to the Flash Memory type. Samsung 64gb cards and some other 64gb+ cards are actually using MLC Flash vs TLC flash (TLC is the reason SSDs used to die so fast at the start).
This leads to 3X+ more the write to the card before its lifecycle is hit and it dies.
Which is good because like i said the 3DS is constantly read/writing to the card. I have personally seen SD/MicroSD cards that came with the 3DS die due to this
Also the benefits of a larger card also come from reading it on the PC. For example my 32gb Card Class 10 caps at 30mb read speeds, my 64gb Caps at 80mb write speeds have a larger gap also.
Sure the 3DS seems to have a hardware Cap of about 3MB/S but the benefits are elsewhere and that is important.
The Boot times you stated are more due to the fact that
LARGER CARDS HOLD MORE CONTENT ofc its gonna have longer boot time when you Home Menu has to read 2x to 4x the amount of content on boot
I saw NewEgg was selling 32GB MicroSD cards for $7.02, I might get two and use the program to duplicate my SysNAND and just swap between the two.....that would help get around the game limit plus give me around 60GB to play around with games
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Honestly Get a 64GB you will not hit the game Limit installing 3DS games unless you installed like 200VC games.
Each AList 3DS game averages 500mb -1.5GB
I installed the Best 40+ games on my 3DS and that hit about 50gb including DLC.