Because removing options from players is the best way to go. That is sarcasm. If the Naga can cause the horde and alliance to lose ships and portals then you might as well just delete WoW from Blizzard servers. Because that is game over. You can't have any new zones, any hope of defeating the naga. Of course you'll argue another lore reason but there are no lore reasons why those zones would be inaccessible. You can't lore away a stupid restriction on game play.
It also isn't about bringing all zones to the current timeline because you want to exclude worgens, goblins, death knights, pandarens, and demon hunters.
In short you have no idea what good game design is. Please refrain from suggesting game design in the future.