Yes, generally speaking flat plate is fine for high seismic regions. You need to follow all detailing requirements for your seismic zone or SDC etc. for your code - other than that no problem. There are tons of flat plate buildings in high seismic regions such as san francisco, some of them very large/tall. Same goes for wind, tons of tall flat plate buildings - probably 1/2 of NYC. Your shear walls will be taking lateral load - depending on your seismic region and local code you may have to design all the slabs for deformation compatibility under the lateral loads for punching shear etc., that depends on your location though.
Not sure what you mean by a problem with doing dynamic analysis. If you mean modeling I would say the only thing off the top of my head is that you should not be modeling the full slab in your dynamic model. Or if you are including it you need to reduce the stiffness significantly. A lot of people replace the slab in a lateral model with equivalent frames using an effective width and appropriate cracking stiffness reductions.
