As you noted, naval SAM systems can do this, thank you for letting me know. What I'm confused by is the idea that an air-to-air missile can or would do this. After learning that naval SAMs can target things so low I'm not going to make any assumptions, so I'll just ask: what sort of air-to-air missile system would be used to target a vessel a few metres above the sea level, and in what conditions could that happen?
Virtually any sort of contemporary air to air missile (WVRAAM, BVRAAM) can target a sea skimming target (whether it's a cruise missile or a large ekranoplan), if it's launched from a aircraft that is within its engagement envelope. Naturally that will differ depending on whether it's a fixed wing aircraft or a helicopter and the range of the missile itself, but generally speaking for the purposes of discussion, if you are a semi modernized 3rd generation fighter aircraft (think J-7E) equipped with something like a PL-8, you will probably be able to target a sea skimmer if it happens to be within envelope for you to be vectored for intercept.
Anything more capable than that -- 4th gens, 4.5th gens, with more capable missiles like more modern WVRAAMs or let alone ARH BVRAAMs -- will be even more capable of targeting sea skimmers than the aforementioned modernized 3rd generation aircraft.
If the sea skimmer is higher speed (supersonic for example) or has signature reduction measures, then your interceptor aircraft and air to air missile will need to be correspondingly more capable, as well as ideally having more forewarning (datalinked in with supporting AEW&C, naval and ground IADS etc to enable better intercept flight paths etc).
So really the better question to ask is -- what sort of air to air missile system would be
unable to target a vessel/missile/ekranoplan that travels a few meters above sea level??
And the answer is -- very few.
Think of Ekranoplans as having most of the disadvantages of a fixed wing aircraft in terms of vulnerability/damage resilience -- that is to say, it is basically able to be mission killed if not outright destroyed by a relatively low mass air to air missile or SAM (as opposed to proper naval combatants, which required much heavier AShMs to damage or destroy)...
... while also having most of the disadvantages of surface vessels -- e.g. to operate at essentially sea level of surface vessels -- without having the endurance of surface combatants or the mass (payload, sensors, damage resilience, fuel) and unable to operate effectively in anything beyond benign sea states.
Alternatively you can think of an Ekranoplan as a fixed wing, relatively slow speed aircraft that has to fly at sea skimming altitudes, with its only comparative advantage relative to a normal fixed wing aircraft being that it can be larger and have greater endurance (but still lower endurance than a proper naval vessel).
The applications of such a type of platform is rather limited. The only practical use of it I could see would be if it were scaled up sufficiently to operate as a transport for very benign sea states in an environment where you have complete air and sea control.
I cannot see such platforms being useful in a combat role or even combat support role.