I'm of the following opinion:
If you're an experienced enough DM then it's not difficult to make monsters that are only harmed by X, or for whom X is needed to make the encounter winnable. X typically has to be part of the plot in these situations. There have to be hints that X is needed in the encounter or lead-up to the encounter, and X has to be available somehow.
An inexperienced DM will use the monsters straight out of the book.
Suppose the book has monsters that are invulnerable (or heavily under-valued) unless you have X. The inexperienced DM will possibly use one. He will most likely not put X in the game, and won't work the warning signs about not having X into the encounter. There's a good chance a TPK will occur. An experienced DM won't do this, but we've already established that he's not gaining anything from this scenario - he already has the ability required to add this special ability to monsters.
Additionally 3e had golf bag syndrome for this very reason - the out-of-the-book monsters commonly required X, Y or Z to kill, so everyone carried an Alpha-Omega of weapons around with them at all times and things got a little silly.