That depends on how you view what you do. One type of person may want to track how well they do at the table by way of how good they make decisions. Winning and losing, and battling it out at the felt. Winning a bad beat, or part of it, sure as heck has nothing to do with your ability. Thus, the winnings from a bad beat would clearly skew your over-all numbers. Your hourly rate, your monthly and yearly numbers are all affected. Are you really making $xx/hr? Or did you throw in a lottery ticket?
Now, if all those number mean nothing to you, and all you are doing is tracking how big your bank roll is, then just throw it with everything else.