Fabian,
The short answer is "yes". In fact, I just submitted an abstract to the American Modelica Conference in October showing in part how to do this type of analysis (assuming they accept the presentation!).
You can certainly simulate the model in SystemModeler (WSM) and take an FFT of the response in WSM to get vibrational frequencies in WSM without leaving the program.
The other approach is to construct a WSM model and import the equations of motion into Mathematica (MMA) and compute the Eigenvalues of the imported system. If the system is nonlinear, you can linearize it in MMA. My presentation will show exactly how to do this (and more). I was going to turn the presentation into a post here on the forum as well. In the interim you can see this older post that I made a while back about how to get equations into MMA. I have improved some things since then but this post will get you started.
http://community.wolfram.com/groups/-/m/t/1214429
Regards,
Neil