Sounds frustrating. If the clutch is worn out, the most likely symptoms would be abnormal noises, slippage, shuddering, or loss of adjustment/travel. Worn thrust brg would be evident from noise and/or heavy clutch. Therefore an inconsistent take-up (with no other worn-out symptoms) would still normally point to the hydraulics.

Is there any other sign of a hydraulic problem - loss of fluid or leak-down? Does the subsequent take-up behaviour vary with the speed at which you depress the clutch?

As you are committing to repalce the hydraulics, would an option be to do the master/slave cyl first and see how it goes? These could be done without disturbing the clutch, so it should be a relatively straightforward matter - compared to getting at the clutch itself.

If you go for the clutch, replace the thrust and consider the rear main seal.

If I replaced the clutch and hydraulics at the same time, I would lose sleep over which of the two cured the problem!