If that's the case, I now hate my SD card xDNope, mine only takes maybe 15-25 seconds for the first mission of a game session. After that they only take 8-13 seconds for whatever reason.
It's a PNY SDXC Class 10 U3 formatted with a 32k cluster size, if you're wondering.
I use a 128 GB Transcend Class 10 USH-3 SDXC card, so it's nothing slow by any means. All my games are playable, but this game has really long loading times sadly. Good thing I have it on N3DS.
I even added all my games all at once to prevent fragmentation.