Radar, IFF, and Jammers
Modern day radar and a civil IFF system would work fine for keeping track of them, assuming none of them are actively trying to evade detection. And if they are devious and turn off the IFF, modern radar can easily detect (and engage if linked to a SAM) something the size of a horse. It has to do with the aircraft's (dragoncraft?) radar cross-section, or RCS, but more on that in a moment.
Put a radar site on the highest point of the island group (or of each island, depending on how distant they are from each other) and rig up a collar/bracelet/vest or whatever to carry the IFF package (Raytheon claims to have the world's most compact version) and some sort of battery/power source.
As for defending them from less-than-friendly AAM's and SAM's, a high-end, high-power jamming system would be my suggestion. Once again it comes down to the dragon's RCS. Note on that site that the average human has an RCS of 1 meters squared, a bird of 0.01, and an insect of 0.001. Meanwhile an F-16C (developed in 1984) only has an RCS of 1.2 and the stealth platforms are much smaller (take the numbers for the stealth aircraft with a glass of salt, as all those numbers are still classified).
So back to defense, shooting down a missile with another missile is a last resort. There are systems designed to do exactly that, and they do it well (CIWS), but they're all ground or ship based and usually require the missile to be headed right for them. Put those on all of your islands, near whatever counts as a population center for the dragons.
And so a jammer, use electronic warfare to counter any errant radar-guided missiles. It wouldn't do anything from heat-seeking IR missiles, but those are short range and your radar system would generally be able to see the launch platform well before it could become a threat. I would have your FOUNAD group operate a jammer fleet out of a dedicated airfield in the island group (along with a few interceptors).
That would pretty much cover most long range anti-air missile threats against the dragons themselves. Just be aware that countering an actively aggressive hostile nation-state (if that becomes a thing) would be a whole different issue. Anyone dedicated enough, or at least with enough reason to do so, and a standing military, would steamroll a PMC such as the Foundation sounds like (advanced tech or not).
Edit: Like Demigan mentioned, I neglected to add the Patriot and S-400/SA-21 systems to the list. THAAD isn't really a contender as it's a ABM system, but the other two are outright nasty against aircraft and cruise missiles. Not sure how or if they could do against a small AAM, but a PAC could hit an S-400 (supposedly) and vice-versa (supposedly). Not sure either has ever been tried. Pop a few PAC-3 or S-400 systems (or PAC-4/S-500 if you want to get some future tech, both are in development at the moment) down on each island for a true layered defense.