Are you referring to the colonists from "Journey's End" who were primarily of Native American descent? I haven't seen the episode in a while so I don't recall if any details were given about the DMZ (other than the prospect of switching some of the border colonies), but I'm not sure their lineage would mean they're descended from pre-UFP settlers.
This is often a source of confusion - but "Journey's End" described a situation that only passingly involved the DMZ. The premise of that episode was that a fixed border would at long last be drawn between the two expansionist powers, UFP and CU; that a DMZ would be drawn "along the border"; and that the shape of the border would be simplified by ceding some UFP worlds to CU and vice versa. The populations of all the ceded worlds were to be evacuated (Nechayev said the colonies would have to be "moved", and she wasn't talking about moving entire planets), but the Dorvan V folks ultimately decided to stay on their formerly-UFP world and become Cardassian citizens. We never heard of them again...
Dorvans being UFP, and furthermore not being the descendants of ancient settlers, is clarified in Nechayev's briefing:
Picard: "This border will put several Federation colonies in Cardassian territory... and some Cardassian colonies in ours."
Picard: "Dorvan Five... that's where the group of North American Indians has settled, isn't it?"
Nechayev: "Yes. They've been there for about twenty years... they've established a village in a small valley on the southern continent."
That these people are UFP citizens is not explicitly stated in dialogue, but Picard later insists that the planet is "still Federation territory" when Gul Evek makes threats.
As for the lineage of the Dorvans, their leader says they left Earth 200 years prior in search of the perfect new home. Nothing indicates they would have been stuck in a spaceship for that time, though; probably they moved from place to place. After all, the UFP had the chance to warn them about the risks of settling on Dorvan V, apparently just prior to them making that ill-conceived decision.
The supply ships had dampening fields to confuse sensors.
That shouldn't be proof of anything, though. In "Rules of Engagement", we learn that Klingons routinely cloak even their nonmilitary shipments. Probably they do this to keep the enemy guessing, or at least annoyed. Doesn't mean they would be up to anything, beyond their usual "everybody is an enemy even if otherwise proven" mentality.