Uldah's Sitting right on top of a Nuclear Weapons Cache....they just don't know it.
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Those could also be wells, with grates protecting you from accidentally falling in.
They're not really designed like typical well systems, especially given their distance and location of most of them (usually far away from the city, and Eorzean civilization is to the point a well system would at least be within the cities or close enough to use Chocobo transport for.)
It's because the world of 1.0 was full of crap, so it had a ton of sewers to fit it all.
Or just bad world design!
This thread makes me wonder if we'll see remnants of the 6th Era as we explore ARR
Its where the ninja turtles live.
We don't know and we may never know. Maybe they're just weird decor, like the random wells and campfires.
Someone should make a list of things that we didnt ever get any real information on... that would be a fun brainstorming session