Ghosts weren't a well documented type back in Gen 1.
People forget that in gen 1 and 2 you are literally discovering new Pokemon or new information about rare Pokémon as you play the game. It's only after gen 3 that we shift to a Masuda world where Pokémon have always been present and we know everything about them.
I wouldn't say the MC in gen 1 discovers ghost types exist but he definitely finds a practical way to identify and demistify their existence, which is why there's no trouble identifying them in gen 2. This explanation no longer makes sense in gen 3 which canonically takes place at the same time as gen 1 since you can see ghosts just fine.
