When I use the word "clandestine," I do mean "secret." The choice of the word "clandestine" instead of a more common synonym like "secret" often reflects a desire for more precise or nuanced meaning. "Clandestine" often implies that something is hidden for a specific purpose, often because it is illicit or unauthorized.
Regarding your question about whether this pertains to clarity and coherence or syntax and diction: it falls under diction. Diction refers to word choice and the style of expression, while clarity and coherence pertain to how well the ideas are communicated and connected. In this case, choosing "clandestine" affects the specificity and tone of the description rather than the overall clarity or coherence of the sentence.