Where have you all people been in the past years that you are puzzled by NPCs highwaking now?
They always have, and the tools for dealing with that are the same. Shoot the FSD, shoot the drives, use a wake scanner and play the game of attrition.
There's nothing to fix here, NPCs aren't supposed to exist just for you to effortlessly farm, despite Frontier's worst attempts at trivializing the game.
Yes, it's true, they have waked out for some time now.
The problem with using a wake scanner is that if they are mission targets then destroying them in a different system to the one specified in the mission doesn't count against the mission - so a waste of time.
And if you get a pirate lord down to 20% hull when they wake out, they return seconds later (in the same system, despite them high waking out) with 100% hull and of course full shields (and SCB's) again.
I agree that NPC's shouldn't be there to be effortlessly farmed, but for targeted assassination missions the high waking out is simply a silly distraction since there's no good way of chasing them or playing a game of attrition.
So for sure, if it's random NPC's that one is farming then by all means have them care for their own mortality. But if they are mission targets they are absolutely there as the player's content. By all means make them challenging, but don't make them waste time.