----1. In an assembly with bolted connections, which is more conservative with regards to the results?
Answer: Assembly with bolt pre-load / torque defined.
----2. If we do not specify the bolt pre-load / torque, how accurate will be the results?
Answer: Depends on the SolidWorks Simulation + your assumption.
It depends on what you are trying to figure out.
I am more concerned on the stresses generated on the components the bolts are clamping (rather than the bolts itself).
Don't let me dictate how you do your simulation, however I would say if the design requires a preloaded bolted connection you should model it as such as I don't know what kind of assumptions, boundary conditions, and bonding you would use otherwise. That being said I guess the easiest way to answer that would be to simulate it both ways and compare the results.
Also the bolts can be modeled as ideal connectors without actually analyzing the stresses in the bolt itself. There are a few methods to do this, some like the "bolt connectors" in solidworks which create unrealistically high localized stresses or creating a rigid (non-deformable) part with force applied as the preload which may create something more realistic at the cost of solution time.