There's a similar issue for the NPCs one can soul trap, since we would expect them to have black souls in later games. So its hard to judge whether or not certain things in Morrowind like the Dagoths might have had black souls or kept the grand souls they had in game. The matter is complicated by the fact that black soul gems only appeared in games after TES IV: Oblivion where they were introduced as part of Mannimarco's necromancy.
In the case of the giants, while they do use tools/have a rudimentary sort of civilization, we don't see anything more than that. In the case of the Falmer, they are corrupted and betrayed Snow Elves (see Knight Paladin Gelebor's description of what the Dwemer did to the Falmer: ) who used to have black souls until the Dwemer betrayed them and did something that made their souls white so the Dwemer could use their souls for their machines. It does indeed appear to be a certain level of intelligence.
