The likely result is that the ramming ship and the ship it rammed stick together in an inelastic collision. Some energy is necessarily lost in such a collision, and the combination of the two ships stuck together will have some velocity. In fact, that energy loss is the energy spent in damaging both ships' internal structures--it's the conversion of velocity and momentum into crumpling and denting and shearing the ship itself.
Say ship 1 with mass [itex]m_1[/itex] is ramming ship two with mass [itex]m_2[/itex] and does so with speed [itex]v[/itex]. Conservation of momentum tells us that, in a totally inelastic collision where both the ships stick together, the velocity [itex]v'[/itex] after collision is
[tex]v' = \frac{m_1 v}{m_1 + m_2} = \frac{\mu}{m_2} v[/tex]
where [itex]\mu = m_1 m_2/(m_1 + m_2)[/itex] is called the "reduced mass" of the system.
The kinetic energy lost is
[tex]\Delta E = \frac{1}{2} (m_1 + m_2) (v')^2 - \frac{1}{2} m_1 v^2 = -\frac{1}{2} \mu v^2 < 0[/tex]
For non-relativistic velocities, this should give a good ballpark figure; the totally inelastic collision assumption is probably only roughly good, and strictly speaking, some of the energy goes into damaging the ramming ship. Take this estimate as an upper limit on the work done damaging the target ship. As has been pointed out, just because this is the energy lost doesn't mean it gives a great idea of what kind of damage results. That energy can be lost in physically deforming the framework of the ship or in melting materials and so on.