While we don't know the specifics of Soviet nuclear targeting (in the Cuban Missile Crisis, or any other period), I think we can safely say "probably not." Why not? Because a) the Soviets had very limited ICBM forces at the time and they could not reach South America from their installation at Plesetsk (they simply lacked the range; they could go as far south in the Americas as North Carolina); and b) Soviet bomber forces could also just barely threaten North American targets, and not South American targets; and c) the US had a huge nuclear advantage over the Soviets (20-to-1 or so) and the Soviets were not yet in an era of "nuclear plenty" when they could afford to target non-combatants (if they ever did).

The likely "order of battle" would have had the Soviets extensively targeting places in Western Europe (NATO and all that), and some US cities. The Soviet ability to target outside of Europe and Asia was quite limited. I don't see them targeting Latin American countries in the 1960s — they're just too far away, and range matters in these things.

(By the late 1960s, the Soviets had nuclear-armed submarines, which changes the range problem quite a bit. But that is later.)