Quay is from a French source: 1690s, variant of M.E. key "wharf" (c.1300), from O.N.Fr. cai (O.Fr. chai) "sand bank," Spelling altered by influence of Fr. quai, from Celtic source.
Yacht is probably pronounced thus because of its Germanic origin: 1550s, yeaghe "a light, fast-sailing ship," probably from Norw. jaght, from M.L.G. jacht, shortened form of jachtsch