You are right, it doesn`t matter. In international waters states can only board ships flying their own flag. They can also board ships from countries they are at war with, but I don`t think the israelis are at war with Turkey :-)
Like the pirate ships everyone's been boarding? Or the Argentine ships that were stopped from heading towards the Falklands? Or the ships that many nations stop and inspect for various reasons?
Perhaps you think, with Hamas doing everything it can to attack Israel that they are NOT at war. OR might as well be at war? The exclusion zone is declared and known. There's no surprise. Ships headed to Gaza to deliver supplies MUST stop and be inspected. There's been too many incidents of ships bringing ordnance into Gaza for anyone to think otherwise.