First of all. After I compiled a plasmoid or program, can I delete the folder with the source code I compiled from?
Secondly, and most importantly, how can I update such plasmoid, for example? Should I delete and uninstall it, and then perform a clean install? Or maybe I can reinstall from newer, downloaded code (without previously uninstalling) and it automatically gets rewritten/updated ?
Yes, it’s safe to remove the source-code folder. As for updating, all you need to do is the third option you listed (i.e. download, unpack, compile, and install). No need to uninstall the previous one first.