Bananas aren't nearly as effective in teams. In singles, because there's only one other person, they're much easier to control and harder for the opponent to deal with, because they can't get help getting out of them. In doubles, their partner can intercept a banana to help your opponent, and because everyone else can slip, you have trouble keeping control of them. It's too easy for someone else to grab your bananas in doubles. Plus, you could make your partner trip, and that's never good.
As Bellioes said, the cons seem to outweigh the pros. Not that you can't use bananas in doubles, but you don't want to have two out and glide toss and dribble all over the place like you would in singles. You'd most probably just use one to set up a quick combo, and one for the kill. And you have to be careful and pay attention, because it's too easy for your oppponents to get control of the bananas by having one sheild and the other grab, and your teammate can trip on it and get killed.
But I hardly use Diddy for doubles anyway; I use Wario for doubles. It's just the few matches I have played as Diddy in doubles, you can't use the bananas as freely as you would in singles.