Softbricking a 2|3DS with custom firmware is not easy; you would have to ignore warnings and do stupid things on purpose like deleting or modifying files on the internal NAND. But even the worst softbricks can be repaired relatively easy with ntrboot and a NAND backup.
An example for such a stupid thing would be hex-editing or overwriting [S:]/twlmbr.bin (although this seems to be just a normal MBR I blacked out the actual data in the 66 bytes leaving only the 0x00 bytes visible)
You have to force these things. It can't happen by accident.
Speaking of the NAND: The actual modification (B9S) is written to the internal memory of the console. There is no such thing as a “modded SD” (though boot.firm is needed on the SD to boot the device until a copy of boot.firm is put on CTRNAND). Just follow the guide from the beginning to the end, don’t omit any steps (including SD test and NAND backup!) and everything will be fine.
If you have any further questions or problems just ask. Have fun!
Make sure that your SDcard is real... For 1TB i would recommend you to do a h2testw before as there's a lot of fakes... If it is real (in my knowledge there's only Lexar with a full size sd... ), then it should work (not sure what is the 3ds's maximum though)
At that size, a genuine 1 terabyte sd card would work but be impractical to use because of dirt slow load times. Only a few flash memory companies make cards at that capacity. Brand new, real 1 TB SDXC (micro)cards cost around US $350 MSRP. I would not trust buying a card at that size and then using it until it passes hardware check in H2testw.
You're better going off with a 128 GB card formatted in FAT32 + 64 KB cluster size: good balance of space versus speed trade-off.
200-256 GB card could work if you're the more patient type of person.
Check my signature for sd cards, or visit your local walmart for this new brand.