You will not find a satisfactory answer from others. I can only share my experience with you. If the mod authors of the Nexus mods have adapted them to the newest Larian patches & hotfixes (which takes time) then I would always give them priority if there is no mod.io version. Some mod.io versions are also worse than their Nexus originals. I had recently tested this with some mods before the recent hotfix. Most Nexus mods are also not yet available as mod.io versions and will not be, as mod.io is said to have too many restrictions... I am not a modder myself, but I have no doubts about the statements of these modders.
This can be frustrating as I myself have been playing BG3 for years, i.e. since EA, and hope for a stable final version, as I am unfortunately dependent on mods that make the game playable for me at all (e.g. party size, 5e spells).