Cardio? Doubtful to say the least.
I find a good session tends to pop a few creaky stiff joints into place, which is always great. Keeping the knees lubricated probably isn’t going to hurt you as long as you don’t play 8-hour straight sessions every day at which time maybe you want to scale back or break it up a bit. 
I believe at least in the early stages of learning there’s a lot of hand-eye coordination going on that’s not found in the same way for yoyo. Yoyo is a reactive and predictable thing… before long, you land a trapeze (as a simple example) because when you swing around and apply just the right tension, the yoyo almost has no choice but to hit the string. It’s a muscle-memory and “feel” thing.
With kendama, at least as a beginner, I’m definitely AIMING for the hole when I do the spike that ends an around the world. Not quite the same for basic pull-up spike, but the sideways ones where you are looking at the hole and trying to stick it? Hand-eye coordination all the way.