Do any of those switches actually do anything?
Yes, meanwhile most of the switches do what they did in the real spacecraft. We simulate most of the subsystems (GNC, SCS, EPS, ECS, RCS, SPS, TELECOM, SECS etc.) extensively, but of course there are some odds and ends we need to clean up before release, mostly unwired circuit brakers.
What I mean by this is that so what if I don't switch on the pyro arm and logic sequence before a launch. Or I've launched without setting the FDAI.
Nothing, the Saturn doesn't care, the CSM is mainly just a payload during launch (except LET jettision).
Or do you simulate an over pressurisation of the O2 tanks. Can the simulator allow you to relieve this pressure.
Yes, you can overpressure the cryo tanks with the heaters/fans, but they don't explode nor trigger the burst valves yet.
How far do the mechanics "behind the scenes" go in NASSP. does it calculate temperatures, pressures and thermodynamic responses or is there just a switching order which makes things work.
Another way to reword this question is this: The dragonfly is simulated very realisticly including things like venting fuel causes thrust and fuel cells depletion affects systems etc.. does NASSP do this?
Actually, we're using the same system as the dragonfly, Radu Poenaru's
System & Panel SDK (SPSDK) in a heavily modified version, so all the things you mentioned are simulated properly. Look here for some things you can play with regarding temperatures, pressures etc.:
http://nassp.sf.net/wiki/Electrical_Power_System_(CSM)
http://nassp.sf.net/wiki/Environmental_Control_System_(CSM)
Our biggest problem currently is the lack of comprehensive documentation. For example the RCS has been finished a couple of months ago and is now working realistically, but I'm still writing on the documentation. The only subsystem with a wiki article as it should be is the SPS:
http://nassp.sf.net/wiki/Service_Propulsion_System
Look here for an overview of all CSM systems related articles:
http://nassp.sf.net/wiki/Category:CSM_systems
Just in case I didn't mention it already in this thread

, the biggest highlight is the Virtual AGC, of course. It's an Apollo Guidance Computer hardware emulation and runs the original Apollo flight software, Colossus 249, most probably used for Apollo 9 and the only part of Project Apollo - NASSP which is no simulation, but the real thing.
Cheers
Tschachim