I considered microchipping my bunnies awhile back. I don't think it bothers them any more than it would a dog or cat.
I was told when I was researching it that the problem with it is that it's still a pretty uncommon pratice to chip rabbits, and most places (even shelters) don't bother checking rabbits for the chips when they come in.
I guess it would really depend where you live, and if he ever got lost, who picked him up. You might get lucky and the particular shelter/rescue or whatever might check him, but they might not.
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