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The reason it only happened once in 7 years is because (rightly or wrongly) managers never allow themselves to be put in that situation on a regular basis. If every team had only 2 catchers and one of them DH'd 50% of the time, then it would happen more often. And no manager wants to be the one with his job on the line when his pitcher has to hit in a close game.
Another reason it's so rare is because there aren't many C that you absolutely don't want to lose their bat from the lineup.
Obviously, if Mauer can't continue to catch 120 games a year, then the Twins will be in the same boat. Will they have him DH 50-100 games per year and not have a third catcher? We'll have to see. I bet on the third catcher.