Its not always guitars in particular, though I know what 60 cycle hum sounds like coming from a strat.
Most of my good starts I modded with grounding shield (copper paint/copper tape).
More often than not its the Amp sim itself and its only using high gain amps and/or associated with gain pedals in general.
When im using high gain Amp sim models I always use a gate. most have them built in to the amp sim for this reason alone.