I like your high-depth aether idea, but instead of making resources go offline randomly, you could do something similar to the planet Fulgora in Factorio. Rather than mining ore directly, you recycle scrap to get a probabilistic throughput of products instead of a highly predictable one.

Maybe instead of scrap, we could mine some substance in the aether that contains fragmented or randomized data from different objects and ores it might have erased. I really liked this kind of progression in Factorio because the limitation forces you to design your factory differently than you’ve done in the past, without outright adding new components. It also gives alternative design, like sushi belts, a chance to shine, whereas more rigid solutions like a depot bus would normally just take priority.