We report on collision induced fragmentation of isolated molecular nanosystems studied with an event by event detection technique including the correlated detection of both neutral and charged fragments. This work focuses on the dissociation induced by collisional excitation without ionisation and electron-capture. Two molecular cluster cations are investigated: the collision of protonated hydrogen clusters at 60keV/amu with helium targets and that of protonated water clusters at 8keV with an argon gas. In addition to the molecular evaporation process the dissociation channel leading to the production of the H3+ or H3O+ molecular cations (loss of all the molecules) is observed with an unexpected abundance. The cross section for the production of these cations is observed to increase with the number of molecules in the cluster. Such an increase cannot be associated with the direct collisional excitation of the cation core of the cluster.