All Strongholds look the same to me - if I come to one after one enemy has been defeated by another enemy, is there some indication it is the Lord's/Master's original stronghold and not one they conquered? Wouldn't want to spend 7 turns sieging a normal (though profitable) province. This hasn't happened to me yet, but I think I've been lucky - on a couple shards I've had an enemy be defeated before I even met them.

The home province containing the stronghold looks more built up than the normal ones in the map, and has multiple flags if you look closely. I don't believe that forts, etc in the provinces have more than one, though I might be wrong.

There's no need to do that so don't worry.

As Jamotide mentioned Capitols (aka main strongholds) do NOT show extra building on the overland map and more importantly in the little box info you can access on any province you can see.

You notice when you highlight a province ownded by an opponent that on the bottom right of the screen you can see 4 boxes of info, the last one on the far right is number of sites found so far, the 3rd one is type and str of fortifications, the first one is type of guards, and the 2nd one shows how many structures are build. On main capitols this is always blank wheras on any other province that has say mills, sawmills, Mines or forts their is a number between 1 and 3. Thus if there's a number it's not his main stronghold.