Which books? In Heir to the Empire the ysalimiri evolved to negate the Force around them to hide from the vorksnyrs who used the Force to hunt. Thrawn used them as protection against Joruus C'Baoth and Luke Skywalker.
Yeah, I am referring to the Heir to the Empire Trilogy. Thrawn's master plan is to grow a Clone Army, and once he finds Wayland's location with its cloning facility he starts harvesting ysalimiri. He didn't know he would find C'baoth there, but had contingency plans if he ever discovered a Dark Jedi to team up with.
And I don't think he ever worried enough about Luke as the last Jedi to make a formal plan against him. The ysalamiri he carried around on Fleet ships were protection for the crew from crazy C'baoth as he learned to coordinate individual Imperial minds.
(In the end, I don't think the crates on Ahsoka have ysalamiri in them...that would have needed set up or referenced by Ezra in some way to work...)
Thrawn picked up the Ysalimiri because he knew (or at least had a strong suspicion) that Emperor Palpatine had left a dark side force user to protect Wayland. Thrawn used the cloning cylinders to clone his best troops so he could crew the dark fleet quickly. He made a bargin with Joruus C' Bayoth to use battle meditation to help coordinate his troops and offered up Luke Skywalker as a psooible apprentice for him.
As far as the caskets, I'm wondering if they are more night sisters. Thrawn mentioned waking up the three mothers shortly after his arrival on Peridia.