1. Disabling the upcycler via circuit network should also disable the requester/buffer chests. For example upcycler for electromagnetic plant would hold 1.8k holmium plates - meaning you can't craft anything with bots until this is satisfied.
2. Consider adding an option to disable buffer chests with the circuit network. Could be a separate signal in a limits constant combinator. I had about 200 EM plants, before upcycler started, then it ate everything :)
3. Does it make sense to make separate loops for different qualities with items going between loops with splitters/inserters? While I had EM plants - the belt was full of low quality materials to the point it couldn't offload high quality materials from the recycler.

For the point 1 and 2 I need to check the API if is possible, I don't know if is possible to disable a logistic chest in game without changing the requests?

For point 3 I'm not understanding, multiple loops? I think that's a re-design of the mod, I may skip that. But try to upgrade the quality of the inserters to have faster inserters and use the latest tiers of belts, they should clear the loop quicker.

For points 1 and 2 - you can connect logistic/buffer chests to circuit network and enable/disable it as usual on signals.

For point 3 - consider this diagram - inside of a loop there's recycler/assembler. As long as the ingredients are normal - there's no point for them to travel past higher quality consumers, so in the middle bottom there's a splitter that routes normal quality up and anything higher to the right. This way items with the same quality mostly sit within their loop, get consumed faster and don't interact with other qualities except for cases when quality went up, and even then - they go up to splitter and leave this loop.

<--- <----
v  ^ v   ^
v  ^ v   ^
---> ---->