Are dark stains that show up when wet embedded mold?
All wood products are loaded with mold spores. 
I work in a lumber mill all the lumber is sprayed with a fungicide to stunt the growth for a month or two. When the wood is dry and not exposed to moisture there will be no growth. There hundreds of different types of mold and only a few are hazardous, so yes there is mold and fungi in your wood. Do you need to do anything? No . You have fixed the moisture problem now close things up and don’t worry about it. Untreated wood at the mill is black in a short time. When I worked n ply wood actual mushrooms would grow in the edges of the veneer stacks. 
Not trying to scare you but the only way to get rig of the mold and fungus is to replace the wood with metal.