I know added mass should taken into account, so undamped eigenfrequency can be calculated, but how to deal with damping? Is depth of water an important parameter?
I hope that you already found a solution since it has been almost a year since your question. There are several well accepted software tools used in industry for marine structures (jackets). Depending on the site conditions there will be an interest for either wave - wind - current loading condition or seismic ground motion induced loads. From Kasiphon K comment you will see that soil induced damping if far higher than hydrodynamic. I believe today you can model fully "interconnected" jacket - foundation analysis with soil - structure interaction tools available through commercial software (SACS, Abaqus, etc).