Yes, the hydrodynamics in galaxy collisions can be very important.
Unlike stars, the gas in galaxies can dissipate energy through
shocks during the collision. WIthout going into the details too
much, basically interactions and mergers seem effective at
triggering inflows of gas into the central regions of the
galaxy and/or merger remnant. This gas may fuel starburst or
feed a black hole. Some of the most energetic beasts in the
universe show evidence of maybe being mergers, and nearbyy
mergers (ie NGC 4038/39, Arp 299, and the like) show large
molecular gas masses at their centers.
If this gas subsequently forms stars (a very likely possibility!)
one might expect to see significant breaks in the luminosity,
metallicity, and age (however you want to measure it) profiles
in the merger remnant.
One current thought is that disk galaxy mergers formed a large
fraction of present day ellipticals. Some ellipticals show
kinematically peculiar cores, perhaps because of an aging population
of stars born in a merger event. MAYBE.
So yes, gas dynamics play a big role in the evolution of merging
galaxies. references? try the two references i've been pushing
throughout this thread: Barnes & Hernquist, Annual Reviews of Astronomy
and Astrophysics 1992, and the same authors in Physics today last spring
sometime (Steinn, do you remember that reference?).