You can do all calculations from 3d to 0d in Wien2k code. Wien2k is a periodic code and it generates an infinite 3D system from a specified unit cell and lattice vectors. Thus, the Surfaces, nanowires, quantum dots, clusters etc can be studied by using slab geometry or spercell geometry. So for quantum dots just prepare your cell with taking a large box and put your atoms at the center of it. Then you have to give your input considering the p1 space group in wien2k(As it does not have any symmetry i.e triclinic). I guess that solv your problem. If you have any query, we can talk offline.
I guess so, although I'm not an expert in simulations. Probably quantum dots is an easier case than thin films, due to smaller number of atoms used in calculations.