Have you detonated any major nukes in the game?
It is possible that the lag is caused by the water movement simulation, which runs for a while after the nuke detonates. This will take a while for larger nukes (100kt or more), so if that nuke was in the 'recent past' - like last hour maybe - then that might explain it. Other than that, I'm running short of ideas. Maybe I'm not clearing a table properly and it has slowly accumulated entries. Alternatively, the game is generating huge numbers of new chunks, and my chunk generation script is causing problems, although I doubt this as that would make your map use huge amounts of space.
TBH, I might need your savefile to get a better idea of the problem.
I would currently guess that the problem is something True Nukes does on its own, with relatively little interaction from other mods, and the problem is just one of scale - your huge play time has exposed a bug which I've never met before.