I'm not going to be able to give you a definitive answer, but I think these are good questions to be asking.
This is kind of a classic tiling problem. I'd suggest looking up Octrees as an example of spatially sorting your entities and managing sub-list sizes. If all your tracking is sector crossings, you could even sort entities so that those closest to sector boundaries are updated more frequently (as they are more likely to cross).
But first, I'd also take a look at the new Entity Component System and Jobs System. I don't know much about them, but I think they are specifically designed to facilitate high performance code design patterns. Well within the scope of your problem.
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