I have the same issue as Maltz.

I can tell if an army stack is infected provided that it has a general or agent with it as the skull symbol appears in the corner of their details.

But if the army is led by a Captain and has no agent with it then there seems to be no indication. Thus moving units into a city for retraining can infect the city as can transferring units from stack to stack.

I only realised this when merging two army stacks and suddenly seeing my general become a plague carrier.

As far as I can see the only way of establishing whether an army without a general or agent still has the plague is to move a general or agent into the stack and see if they catch it.

On a secondary question:

If a fleet docks at a port of a city which has the plague do the ships become plague carriers?

Can they infect other cities by docking at their ports?

Can they infect enemy cities by blockading their ports?