Well we know that and McClane knows that once it's been explained at the police station, but I would assume that SOP for handling bombs is to treat them delicately since they theoretically could be rigged to go off in more than one way.
On the train, McClane handles the bomb more delicately since there are people onboard.
However, McClane does puncture one of the liquid containers later in the movie on the ship where there is less risk of anyone getting hurt, besides him and Carver that is.