An answer to some of your questions (sombody else may care for the others)
- How should encrypted models be used in KiCAD? Can they be deciphered by the simulator (or the plugin)?
Unfortunately this is not possible with ngspice.
- Do all PSPice models work with ngspice? What I infer from the web is that PSpice models are for the PSpice simulators while ngspice is based on Spice3.
Yes. If not this would be a bug, and I would care for it. ngspice-30 has to be used and a compitibility switch set (see http://ngspice.sourceforge.net/ngspice-eeschema.html)
- Again in the Generate Netlist window, there is a simulation command. How can that be used?
Please see my post Multiline directives with an example how to use this button.