Ultimately, as difficult (or easy) on the Steam Deck as it would be on a regular desktop.
For games with built-in Steam Workshop support, it’s as easy subscribing to mods and enabling them in-game as it is when playing on a PC, and for games that don’t have that, you can switch to Desktop Mode - which is essentially a regular KDE Linux installation - and do your modding like on a regular PC.
As for the specifics of modding Morrowind, though… with Bethesda games, you can go absolutely hog-wild with mods, or you can just chuck a handful of QoL ones in and call it a day. Last time I’ve extensively modded Morrowind, it’s been couple of years back, and there’s been all sorts of tooling developed - you’ll need to read a bit into how it works nowadays, and how well it operates on Linux
This little snippet covers how to get Syncthing to run in background on boot regardless of Desktop environment (so that you’ve got full synchronisation even in default game code), might be worth adding it under the link to Syncthing. :)
https://gitlab.com/-/snippets/2363444