There are some issues, such as slower load times in some cases and a few CIA managers crashing with SD cards greater than 99 gigabytes. However, the slowdown isn't really that bad and only happens in a few places, and FBI handles large cards just fine.
If you have a lot of things installed, home menu might be slow at loading the icons, but this is less of an issue on the n3DS. I wouldn't worry about it.
No. Get a well known brand like sandisk or Samsung brands and you'll be fine. Also, devmenu and bbm are the only ones with issues of booting with 99gb or more free space. Use fbi 2.0 or higher.
It really depends on the card. I had some issues with really high end (Professional 1000x) 128 GB Lexar cards early this year, but a cheaper 64 GB Lexar worked fine. I recently got a 128 GB Samsung(?) Pro+ that's been running okay too but I haven't given it much of a workout yet.
(Probably the really fast card either needed more power or produced more heat than the 3DS could deal with).
Using a 128gb Samsung evo+ on a n3ds and it's fine. Filled about 60gb of cia installs and get the odd arm9 payload taking longer to fully boot than normal sometimes but functionality wise, it's been fine.
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