While SMS does not support ADCIRC 3D the version of ADCIRC released with SMS 9.2 can be used in to simulate a 3D baroclinic model run, you just need to edit the command file accordingly (which is not straight forward). I suggest you have a look at the ADCIRC development page (http://www.adcirc.org) and specifically at the manual and examples (there is a 3D baroclinic example). In terms of 3D modelling however, don't expect much support from the developers, and non from the SMS support as they only support the 2D version. You will also have to write your own visualization software (suggest Matlab) to view the model solution in 3D.
Another alternative is to try the hydrodynamic model SELFE (free to download the code... you just need to compile), which uses a near identical grid structure to ADCIRC (only boundary header lines are different) and is fast and efficient to run.