MacCaig writes a lot about observing and being observed and the dynamic interaction between the two. Is he taking his mind for a walk or is his mind taking him for a walk? I don't see this so much as a reference to Descartes who compared the mind to a ghost controlling the body (machine). I take it to mean that, as there is no way to separate the speaker from his mind, in terms of doing or thinking or observing, there is no way to separate the observer from the observed: you can't have one without the other. And it is reciprocal when other minds are involved. As limited as a cow's mind might be (relative to a human's, as far as we know), the cow is observing as well. Maybe the cow thought better of it because it felt self-conscious mooing in front of all this natural splendor, or maybe the cow just had a moment of existential freedom and simply preferred not to moo for no other reason than choice. The overall point, for me, is that the cow is observed by the speaker but the cow also does some observing. And that means the cow is aware of itself and the world around it. Awareness of being observed and observing: kind of a round about way of showing interconnectedness.
Of course, different people can interpret poems differently. My opinion is that this poem is about how difficult it is to actually know things and how difficult it is for us to make up our minds.
The poem is full of images of uncertainty. The cow is one of these images. It is quite an amusing image -- the cow starting to moo and then stopping -- but it helps to reinforce the theme. In this poem, nothing is certain. The speaker is never sure what he is seeing, the ducks and the water shilly-shally, the cow rethinks his moo.