The penalties for a stack commander not being activated are:
Reduced movement (-35% speed) --unless in PP.
Combat penalties in hostile regions (up to –35%) [I understand this to mean, that it is dependent on the MC the stack has in the region. I believe I actually read this in the forum somewhere.]
Offensive posture prohibited (not applicable for admirals).
So, until an assault occurs, the activation status of a stack commander is irrelevant, these things are:
Sieges and breaches
If the besieger decides to assault the Overcrowding Rule
will take affect.
I'm not sure of the penalty for being un-activated, because that penalty pertains to the region and the combat during an assault takes place inside the location, which the defender controls to 100% --because it's always an either/or proposition.
Maybe Pocus can say whether this is the case.