Seriously, where the hell did it all go?!?!

Shrines and towers are easy, at the beginning of BotW when you activate the great plateau tower all the other towers and shrines are seen rising from the ground so I believe that they just went back due to the calamity being over. the working guardians went back under Hyrule castle to the underground observatory, the broken ones were scrapped for any working parts. idk for sure about the divine beasts tho.

you're probably almost 100% spot on about Shrines and Towers, Guardians probably went back into the five giant pillars that surrounded Hyrule castle, which is where they came from, not the observatory. side point, the Towers purpose was apparently to detect the arrival of Calamity Ganon, and a lot of good they did.

I didn't realize that was where the guardians came from lol

remember, TOTK takes places around at least a few years after BOTW and in the lore if u read it closely u can tell they justs scrapped it all for items and things, you can see parts of the towers and gaudians in some buildings. I don't know about the divine beasts the maybe they died???

they're robots, how would they "die"? imagine if they just simply dumped them in that unnamed landmass to the north of the map.