I am surprised that there aren't problems with leaks. Also 2-litre plastic bottles are not UV resistant so after a summer in the sun I'd think they would be falling apart.
Looks like the bottle is pushed up from the bottom (so the water won't pool around the joint) and then caulked with some kind of sealant. Since these are basically shanties with corrugated steel roofs I would think that leaks would be the least of your concerns. And since plastic bottles come from the waste stream anyway I doubt that replacement after a few years would be an issue. Depends on what happens after a few years of UV exposure... if the main problem is just the plastic becoming hazy, well, that just gives you a free light diffuser!
I think the general idea is that you can reuse any sort of plastic refuse (PVC pipe is also common and it's UV stable), add water to improve the optics, and tada, even, diffuse light without an actual hole in the roof.
Litro de Luz/Liter of Light is the current org carrying this idea forward AFAICT.
The question of leaks is directly addressed, although roof material isn't mentioned:
"You fix the bottle in with polyester resin. Even when it rains, the roof never leaks - not one drop."
Questions of durability are absent, but with the number being deployed, answers should be available shortly:
"In the Philippines, where a quarter of the population lives below the poverty line, and electricity is unusually expensive, the idea has really taken off, with Moser lamps now fitted in 140,000 homes."
It seems the cap is the most UV-sensitive part, and that is solved by adding something to protect it: "The lamps work best with a black cap - a film case can also be used".