He has to whisper all the time, he is either chasing bad guys that he doesn't want to hear him.
Or he is planning strategy with others he doesn't want to be overheard.
Or he is doing things he doesn't want other to know and be responsible for.
Or he could be giving the secret website address of where to get those long life cell phone batteries he has in the show.
I notice sometime Jack whispers even when other people are speaking in a normal tone. Luckily I have good hearing!