Commanders in CK II were something of an annoyance because they often seemed to randomly disappear without trace and so you'd be constantly replacing them - eventually having to spawn new courtiers as you ran out of potential replacements.
Yeah, this happened a LOT to me. I'm still looking for a few of them.
We do have commanders in CK3, but it's only one rather than three per army. Let's hope they don't get magicked away quite so often.