Steel, Dark and Fairy being "discovered" is just a lazy gimmick older games had to explain things that didn't exist in previous entries. Same way how they said in Gen 2 that Prof. Elm discovered breeding or something like that. They're just devices to explain new stuff and mechanics to the player.
Realistically, it wouldn't make any sense for Magnemite to suddenly start resisting a lot of types just because people realized it was also a Steel type, or for Clefairy to be weak to Fighting for five gens then start resisting it and becoming weak to Poison just because people discovered the Fairy type.
It's easier to believe that those types allways existed, just like many Pokémon that were introduced as newly discovered species, or species exclusive to their regions, in their respective gens allways existed as well.