I wouldn't think so, no. All of the current settlements all befell some horrible tragedy and are abandoned. I think it would be weird to drop in on an INRA site and see NPC Karen walking around telling everyone how specieist we are the that bug lives matter, too.
I wouldn't be
surprised if there was an abandoned settlement type seeded along with the new types and variants to explore.
And it wouldn't blow my mind if existing Horizons settlements were re-generated with the new settlement bells and whistles. After all, size, economy type, security, faction, etc. are all part of the existing info held on the existing settlements, which could all be used as data to procedurally generate updated layouts and facilities. I'm fairly sure the new settlements are procedurally generated anyway...
But yeah, I agree, it's not my minimum expectation.
Also Dav's Hope and the Formidine Outposts were hand-placed, I do believe, with a unique design that I haven't seen elsewhere in the game. They're not generated from the background sim. So I suspect those particular ones might be left as-is, as fixed, handcrafted artifacts, unless they consider it worthwhile to manually update them. In other words, perhaps if they become story-relevant again.
So...
Procedural Horizons settlements: maybe
Hand-placed story-related sites: probably not but... maybe