This is just your personal subjective impression not backed up by any objective evidence.
Have you ever pined down circumstances when this happen?
For example I create client ruler save exit load and boom save is corrupted.
Many problems are associated with AI characters and script does nothing for AI. You can check the script if you don't believe me.
I had problems playing EB without using Client Rulers and none using a lot of client rulers.
I also made few wicked tests like creating lots of client rulers in the same city one after another, fighting with them in battle, adopting to family tree, killing on mass in the same battle making them faction leaders and killing them in battle all to no ill effects.
Since all reported problems are unrepeatable and client ruler script is very straight forward it makes me to believe that there are many factors at work here and pining it all at one simple script is not very plausible.
Edited:
As you can see I am using a lot of not definitive terms. While there are no hard proofs that Client Ruler script is creating all sort of troubles I also cant create test that will definitively prove that it doesn't create any problem.
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