If I had known, I wouldn't of had bought a 128gb SSD Card.
I did some tests on my JapN3DS:
Main SD CARD: 128GB PNY High Performance UHS 1 Micro SDXC I
Main SD CARD: Actual Read is around 30mb/s and Write speed is around 13mb/s
64gb - 7 seconds -> cfwSysnand. (64k allocation unit size.)
128gb - 14 Seconds -> cfwSysnand. (32k allocation unit size)
128gb - 17 Seconds -> USA-Emunand. (32k allocation unit size)
Ill try to change the allocation unit size over to 64k or 128k to see the difference in performance. (Getting 70gb off of the sd card, format and transfer it back in will take some time)
But summary, Go with the 64gb.
=EDIT=
Modifying the allocation unit size to 64k increased Emunand load by 6 seconds
SD Write speeds increased to 17mb/s
128gb - 10 Seconds -> cfwSysnand. (64k allocation unit size)
128gb - 11 Seconds -> USA-Emunand. (64k allocation unit size)
I am happier* now.
*wish* I could set it to 128k, but have not found the way to do it. If anyone knows let me know.