I have no expierence with the steam deck, so dunno what’s up with that. Never expierenced something like that on my PCs tho.
Yes, the flags can be unintuitive for beginners, S stands for sync, which will sync the package(s) specified thereafter with the remote repositories. If the packages aren"t installed it means installing them, if they are already installed it means updating them to the version that is the latest version in the remote repository. Full system update is done by pacman -Syu, where y tells pacman to synchronize the package lists first and u selects all packages that are older than the ones in these package lists for the S.
You can easily learn all that by using fish (or zsh with a sufficient config) instead of bash. Then, you can enter pacman - and hit TAB to get a list of allowed flags and a brief description. Choose one, hit TAB again and get a list of flags that go with the one you selected before, again with a description right out of the man-page. BTW, that works with a lot of command line programs and is imo almost necessary to get in touch with the shell.