Hmmm, this one is kinda hard because Nintendo designed the connector really badly. They only fixed it on the OLED and lite models.
It could be:
1. Bad placement of sd card reader
2. An actual pin is missing
1 can be fixed by reseating the connector or replacing the reader
Now 2 is tricky because Atmosphere kinda doesn't support it. When it tries to get keys, it doesn't load. I had to ask CTCaer for help since it crashes on my old Switch. He gave me a special Hekate build that dumps the keys or something and stores it on the SD card. Atmosphere not supporting 1 bit mode started around FW 9 iirc on a later atmosphere release.
Your options if no. 2,
1. Find a cellphone store to somehow bring back the pin or solder all the wires directly to the connector of the reader.
2. Get a bigger SSD and use that (personally did this one and use SD card for small games and gave it to my brother). Don't even think of putting large games on the SD, it takes forever to load games like Xenoblade 2.
2 means no emummc, so you can't use it legitly due to hard drive being bigger than normal.