For modding cyberpunk specifically, Nexus mods has a linux and Steam Deck compatible mod manager. It doesn't support that many games, but Cyberpunk is supported.
I don't have enough experience using Vortex to give much advice for other games, I usually just install mods manually instead of using a mod manager. That said, I know SteamTinkerLaunch is a tool that can be used to run both Vortex Mod Manger, ModOrganizer 2, and some other mod managers for games. Once installed you can select to run games with it from the game's properties menu in Steam. Launching the game will then open a menu where you can select to run a mod manager for the game, launch it without mods, or several other options. There should be tutorial videos on youtube and other places for it.
Decky has a ton of plugins available, you can change how the Deck's UI looks, change game art, change bootup animations, and do a lot more. You can browse plugins here. Occasionally decky or plugins will break when SteamOS updates, and the more plugins you have installed the more likely you are to encounter an issue like this. Some of the plugins are fantastic though so I consider it well worth the occasional trouble.