[Having Problems]
The mods that I've always had in common with your lineup are: Dynasector, BRDY, Interstellar Imperium, LazyLib, Nexerelin, Shadowyards, Version Checker, and GraphicsLib.
I've been having the same issue as you concerning the late game. At a campaign's start I can go multiple hours without a freeze. Later on, I can barely manage 30 mins. From my testing the cause has been campaign-map related, and that it tends to occur at certain intervals rather than just randomly at any time (for example, one save I had a 75% chance of crashing in the next minute... but after that, absolutely no crashes for the next 10-20 minutes past that one minute).
The starsector log always ended with around 50 "updating bounty probability" events after the game froze, which has led me to conclude it's too many bounties probabilities being processed at once. (I don't know if other events are calculations occur at the same time as these bounty update events, so I can't say if it's the bounty probabilities themselves or another type of event that gets calculated at the same time).
I suspect -- and this is purely speculation -- if you could figure out a way to greatly reduce the number of "updating bounty probability" events in the universe at once, it may solve the problem. Unfortunately, the DynaSector only has an option for reducing the number of active bounties (default: 6), and not the maximum number of bounty probability calculations.