Kind of of a nitpick, and I'd doubt they'd fix it but...

[Cybermanderoid]

Why is there two areas in the game called Windurst Waters? Also for some reason I can't find the the option for the second Windurst Waters with the Rhinostery in the crystal teleport options, unless I'm missing something.

[Pixela]

There is only one, however there are two maps for north and south.

There is a time travel version of the zone in the past, but you won't see that until you make progress in wings of the goddess.

[Cybermanderoid]

For anyone starting out they'd be confused, because neither maps mention a North Windurst Waters and a South Windurst Waters, so if you're reading a quest wanting you to go to Windurst Waters for an npc you're left on a wild goose chase until you get to the right Windurst Waters.

[Alhanelem]

Why is there two areas in the game called Windurst Waters? Also for some reason I can't find the the option for the second Windurst Waters with the Rhinostery in the crystal teleport options, unless I'm missing something.
Because there's a Modern Windurst Waters and a Shadowreign Era Windurst Waters (Windurst Waters [S]).
The latter is part of the Wings of the Godess expansion and you have to visit that version of the area before you can teleport there.

The areas are not the same and serve different purposes, which is all I can say without spoliers. All you need to know for now is there's a reason there's two versions of this location and you will discover that in due time.

It's also possible that you're referring to the two different sections of Windurst Waters. The area has two maps due to its shape. You can only teleport there after you interact with the home point in that part of the area. It was a design decision. The map with the exit to West Sarutabaruta is usually referred to as Windurst Waters (North) and the other section is usually referred to as Windurst Waters (South) when referencing the area in wikis and game guides. However, functionally, it is still a single zone, there is no loading screen / fade to black when moving between these places.

[Tarmarkvar]

For anyone starting out they'd be confused, because neither maps mention a North Windurst Waters and a South Windurst Waters, so if you're reading a quest wanting you to go to Windurst Waters for an npc you're left on a wild goose chase until you get to the right Windurst Waters.

Sometimes yeah. Sometimes the person who wrote the quest will mention which part of Windurst Waters to go to.