I am afraid that`s a No to ships ramming each other.
As for Siege weapons on ships - same as on land. This goes for any other units - they can all be individually selected and tasked. When u control the ship full of untis it`s quite simple really - click anywhere on the ship to select it - the sails, the body of the ship e.t.c, or click on any individual unit on the ship to select it - or use drag and select for select some/all units on the ship.
With regard to Ranged siege having limited ammunition - we are actually toying with this idea, most likely Catapults, Trebuchets will only fire if player has sufficient Stone resource. But things can still go 50/50 on this.