Can you target ships that are being played and are on the pile or are they already considered docked and therefore untargetable?

Yes you can. The ships are not docked until they have entered play, so you can target them with news such as Exiled from the Empire, Depleted Resources and Pirate Mercenary before they come into play. The only exceptions to this are Megathron and Thorax, who specifically state that they cannot be targeted by news.