Yes. I would go further and say that there should be many ways of interacting with most of those minor factions and unique features. I could defeat the corsairs and perhaps take their store of loot as my prize, or as you say get some nice naval tech from it. Or maybe I could pay them tribute in return for leaving my ships alone; and pay higher tribute to leave my ships alone and protect my shores! Or pay them to specifically target your enemies. Or if you have a powerful enough navy, you could threaten them into leaving you alone, or threaten them into targeting your enemies. So many options!
A lot of minor factions and unique locations that you can interact with in many different ways would provide an immense amount of replayabiility. It's a somewhat different genre, but HoMM for example has lots of ~unique map features, but there is only ever one thing you can do with them. You can fight the dragons and the dragon cave for great artifacts and lots of resources; you can defeat the guardians of the Cloud Temple for control over a Titan/Colossus/Storm Giant producing structure, etc. How much more interesting would it be if there were many different ways of interacting with these structures?
