Considering there isn’t even multiplayer, I think it may be a good idea to think about what multiplayer might entail before how mods will fit in with it. That said, I imagine mods would work just as they do right now. Both players will likely need to have the same mods to play together.
I would love to see sth like in some terraria modloaders: You can just go on a server and the server tells you automatically what mods to download or (if they are listed in the mods server browser) download them automatically so you can play