How many trains do you have in total ? ( +/-)
Do you have some of them in "no path" or waiting at a signal ? (%)
Do you have some train traffic jam in one of your planet ? ( something broken ?).
https://wiki.factorio.com/Railway/Train ... validation
Path Revalidation 3rd reason => A signal (chain or regular) is created or destroyed (all trains are revalidated).
It seem that you have many trains revalidating their complex path at the same time. I don't think the game knows that placing a signal on a surface doesn't change the possibilities for the other trains, it is the case in your game but it may be different with others mods.
"all trains are revalidated" could be made faster if trains are waiting at trains stations, or a little before instead of being "in a path" such as behind a signal turned red with combinator. That would trigger revalidation on fewer trains.
And if the path were simpler, with less junctions, or maybe using waypoints in some area where it make sense it would make each revalidation take less time.
When you have a train selected, you can see its pathing, the little green or red triangle on the tracks, if there was a meteor to fall on an isolated piece of track somewhere in a densely populated planet, it could block 1 train in a bad spot, which would in turn block many other trains and pile up to create a mess of those path somewhere. If the slowdown is just starting but is heavy, maybe there is such situation that built up since you last built trains, otherwise it may have build up over time as number of trains/junctions increase.