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You're... mostly correct to be honest.
9/11 was kinda the catalyst for a LOT of shit we're dealing with today, so saying Pokemania died because of it isn't that farfetched. BUT at the same time I think it's a bit unfair to blame 9/11 for it when, really, it just comes to the fact the Pokemaina was going to die eventually.
There was a lot of fanbase in the infancy at the time (Sonic, Mario, CoD, Minecraft off the top of my head) and all of them had a big "spike" in popularity before slowly dwindling into a safe platto past 2001, yet all of them have endured and even seen other boosts in popularity as the years went on.
9/11 changed our culture, but people liking Pokemon just doesn't have a lot tied to the War on Terror beyond the games coming out at around the same time. That's like say Family guy got stale because of 9/11. They're barely related.