OED suggests that countable evidences are either obsolete, obsolescent or very specialised.
The countable entries are
†2. Manifestation; display. Obs.
3. a. An appearance from which inferences may be drawn; an indication, mark, sign, token, trace.1860 J. Tyndall Glaciers of Alps i. xv. 99 A day..was spent in examining the evidences of ancient glacier action.
3. b. In religious language: Signs or tokens of personal salvation.
1758 S. Hayward Seventeen Serm. xvi. 493 A person just entering upon eternity..with his evidences all dark.
†4. Example, instance (frequent in Gower).
5. †b. an evidence: something serving as a proof.
5. c. Evidence or Evidences of Christianity , Evidences of the Christian Religion, or simply The Evidences.
6. a. Information, whether in the form of personal testimony, the language of documents, or the production of material objects, that is given in a legal investigation, to establish the fact or point in question. Also, an evidence = a piece of evidence.
†7. a. One who furnishes testimony or proof; a witness. Obs.
†7. b. transf. A spy. Obs.
†8. A document by means of which a fact is established. Obs. exc. Hist. and in legal formulæ.
Of the countable senses not marked as obsolete, 3, 5c and 6 are all specialised uses, and possibly obsolescent. The latest citations which are explicitly plural are 1860 and 1758 [there may be later uses; this is just what's included by OED], which would certainly indicate that usage could be expected to decline.
However, 3a does cover your quote about "evidences of prehistoric settlement". This would appear to be a valid specialised use, and the fact that it is specialised might explain the low incidence.
