So zero pixels means a completely blown (white) pixel? (I would have thought that zero meant a completely black shadow, since that is what has a zero pixel value.)
Anyway, your image was shot with shutter speed 1/125th, at focal length 300mm - and shows pretty clear evidence of camera motion. Is VC enabled? If not, you probably didn't allow enough time for it to settle.
Your shot has some very bright highlights, and they appear to be from sunlight. Sometimes the shot is brighter or has wider dynamic range than any sensor can capture. This very well might be one of them, since in effect you have automatic exposure on. Yes, you're in manual exposure mode, but you also have auto ISO, which effectively means that you're in auto exposure. The camera takes your shutter speed and aperture (btw, f/11 is far more than necessary here) and finds an ISO that yields a proper exposure. Since you were in Matrix and most of the frame is well exposed, that seems to have succeeded to a degree. (It's at ISO 5000, though, so you may well find that there's more noise than you'd really prefer.) You got blown pixels, so the only way to really address this is to shoot with some -EV compensation and then adjust in post processing. (For a landscape, you might be able to use a graduated neutral density filter. But not for this situation.)
I realize that you want something automatic, but there is a wide variety of possibilities, many of which are similar but can't realistically be accommodated automatically. For example, consider a landscape that includes a sunset and reflections of the sun off the water. What is the automatic meter to pick? Stopping down to expose the reflections properly almost certainly yields very dark shadows in much of the scene, and reducing exposure to accommodate the sun is entirely futile. The reverse problem avoiding totally blocked pixels (black shadows). Basically the problem is that there's no way for the "meter" to calculate what's really important in the scene and what to "compensate." (Consider the proverbial black cat in a coal mine - what's the meter to pick? It doesn't know that two little highlights are "eyes.") Active D-lighting compresses the dynamic range, but it can only go so far.
We'd all love a 20-stop dynamic range, but nothing like that is available today. The fact of the matter is that the human eye has a far greater perceptive range than any sensor or film, and to fit scenes into what we have requires some actual photographer input.
_____ Brian... a bicoastal Nikonian and Team Member
My gallery is online. Comments and critique welcomed any time!