Update: the load time doesn't seem to depend on whether the save data is doing a background sync to Nintendo cloud. So isn't a file lock issue.
I wonder if it is something as simple as growing log files like Microsoft word 15 years ago.
I notice the "save data cloud" backup is running really slowly for the problem user account. I'm surprised it's backing up anything because I've just re-installed save data from Nintendo cloud to try to solve this issue!
Perhaps Mojang can allow us to save our worlds out somehow to give a work around for this mess. Either manually in the game ('coz Nintendo won't allow you in the file system) perhaps via transfer to another user account on the device. Or provide realm access as part on the Nintendo online subscription.
Has anyone tried transferring save data to another console? I suspect it'll work like the Nintendo cloud backup. Just wondering if anyone tried it?
The switch 13.0 update has fixed my son's Minecraft load issue (was taking 45 mins to load). Now the game loads in 3-4 mins, logs into Microsoft, all his worlds are still in the list and I think extra packs etc. Data on the console now reads 756 Mb or so, but the switch online backup still says 2 Gb
I'll ask him to play for a bit, and then re-check the on console and switch online data sizes.
Thank you @Gavin Coffey for the update that there was movement on this issue.