I don't really have an answer beyond speculation, however here's what I can understand on how Splatoon 2's online functions.
Your Splatoon 2 data is saved to your system, and when you go online, Nintendo's online servers pulls your character progression from this save data. Nintendo makes the argument that Splatoon 2 is not allowed cloud backups because if a player loses a ranked match they can just redownload a previous Save file and not lose their rank. So since Character progression is tied to the same save file that your single player progression uses that your octo expansion progression uses, that all of your weapons and clothing use. It can't be uploaded to the cloud and the player has the risk to lose all of there data if something misfortunate happens to their system. Its a harsh punishment on the player because of Nintendo didn't have the foresight to divide up the save files, so that character progression in online could be one save file and single player progression/Item acquisition be its own save file. (Kinda like what Rainbow 6 Seige did all the way back in 2015) The confusing part to all of this is that Nintendo does save your character progression separately on a server since this is the information the Splatnet2 App is pulling from, and this server saves literally everything about your character. But for some reason, this data is not what is being used when you go online? It's your local save data? Why save the players character to an online server and not pull from that data when they go online? And if they DO use that data on their online servers why isn't Nintendo letting players back up to the cloud? It makes no gosh darn sense in my opinion and at the end of the day, it just hurts the players.
There are other games that will not be allowed to backed up on the cloud like the upcoming Pokemon Games, because again "It prevents cheating" but I still feel that this is an arbitrary excuse on Nintendo's part.