I had the exact same problem! You probably need to replace the SD card reader in your Switch. Luckily, it's cheap and easy to replace!
However you MUST be careful with the connector. I was too rough with mine because I didn't understand how fragile it is.
I had to buy two new SD card modules because I broke the connector of the first one. I also damaged the port on the motherboard!
Because of all the damage, I had to put a little extra cushion on top of the connector, and now it works properly!
But don't worry! It really is an easy fix. Just be very gentle when removing and inserting your SD card from now on. Even ONE rough push can disconnect the reader!
EDIT: Oh and don't worry too much about SX OS. I thought your post was going to be about a lack of features, and I would say that since their new modchip is coming out, they will continue to support their software for quite a while longer!