first, it kinda was a joke, and second, technically a ghost is not completely "dead", could be defined as a soul trapped between this world and the dead's one (so yeah, not dead yet!)...and I don't think this applies to "ghost" pokemons anyway, since the "ghost" type is more a definition of their nature, rather than an explanation of what they actually are. If you just think about it, a ghost pokemon is not really...the soul of a pokemon who died and remains trapped in some sort of limbo, but more like a creature who lives its on life.
Oh and also...it's an anime, why can't we just stop asking ourselves unnecessary questions and simply enjoy it? (:
i know i didn't realy get to finish this mission but...i'm going to try harder for this next one! it was a fun storyline to read and i had fun reading other's versions of the story. can't wait to read what's happening next.