It’s possible he doesn’t know about the Nightsisters. Or maybe he’s suppressed his presence in the Force in order to hide from them.
They were able to pinpoint Ahsoka’s presence through the Force quickly, albeit while she was conveniently reaching out through it to find Sabine.
But Thrawn told Sabine he didn’t know where Ezra was and that he could very well be dead (and then let her go find him as a means of finding Ezra himself … you’d think he could have asked the Great Mothers to use their magic balls to find him sooner – unless he’s ‘hiding’ his presence somehow, which may also reduce his ability to sense things.
Also, Ezra was still essentially a padawan when he sent himself away. Obi-Wan, Yoda, and Luke were all Jedi Masters by the time they went into exile. That might make a difference in terms of developing your Force senses.
Or, again, it’s just poor writing. Disney really ought to give us ENWorlders a chance to review their Star Wars and MCU show scripts so we can suggest improvements.