I have a small opionion on this subject.
If you look back at Fallout 3 you'll find that the Enclave have pretty much been pulled out from hiding their motives, that would mean that everyong in the Capital wasteland knows of what the Enclave in that regions plan was. This would lead to a large disruption to any remaining Enclave as word does spread easily.
Now if you bring your attention to New Vegas you find that Enclave that weren't even in the Capital Wasteland are running from the NCR, this would mean that it has become general knowledge of what the Enclave's past deeds were, that would mean that all remaining Enclave would have to contend with the BOS in the region as them and the NCR around the wasteland.
Actually unless the Lone Wanderer hands the FEV Virus over to the BoS, the people won't know what the Enclave's plan was; they were going to occupy the purifier to hand out the water to the wastelanders, nothing more as far as they knew. If you read the loading quotes, the Enclave has been mostly forgotten on the West Coast now after the three decades, hence why nobody reacts to the armour; it is also mentioned in one of the endings that people were reminded why they once feared the sight of Vertibirds.
That would make an Enclave force difficult if not impossible to sustain itself any longer, if the Enclave isn't gone yet they are well on their way to being gone, everyone knows what happened and no one trusts them, that also means that they can't get any new memebers(Fallout 3 says they wouldn't want any as they think of all people outside themselves as mutants)
Yes they could still exist underground in hidden bunkers, assuming that the people who live in the area, the NCR in the area, and the BOS in the area haven't already found the bunkers.
The NCR and BoS don't cover all of America and the Enclave don't recruit externally.
If anything the Enclave will probably come back as some new group, changed their names, and changed their tactics to avoid extermination.
The BOS and the NCR aren't even the biggest problem for them, there are still the creatures of the wasteland(If you played Fakllout 3 with Broken Steel or just happened opon an event) you'll see that a deathclaw can take out a few of them, even the Hellfire Troops have difficulty taking them down without dieing.
In the end I would imagine that the Enclave will fade away or transform into an entirely different group all together as they suffer from a lack of people joining, a limited force, a limited world veiw, and not extremely advanced weapons. They are pretty much on par with the BOS exept the BOS could easily outmatch them in sheer force.
That is probably the case, in which case the Enclave will cease to exist; also you mention Deathclaws as a bigger problem than the BoS? Deathclaws aren't so common you know, the Enclave only go near them to enslave them. "A limited world view" :confused: and they are far superior to the BoS in terms of technology, the Enclave have access to a plethora of pre-war goods, superior armour and at least on par as far as small arms go.
In a competant world, the Enclave would have steamrolled the CW BoS in about five seconds flat, even without the orbital satilite.