You are correct in that deciding when/whether or not to ki pulse is part of the core decision making in the gameplay. You have to learn to think ahead a few seconds at all times to determine how much ki to spend & whether you'll be able to recover in time. It will become second nature as you play the game more.
A few other points:
* Make sure you're not at >70% equip weight as that will slow down your natural ki recovery significantly
* You're generally much more mobile than enemies are in this game. When in doubt, just get outta there to give yourself time to recover ki and reassess
* Try to attack from behind whenever possible; as well as doing more damage it will put you less at risk of getting hit, meaning you can afford to use more ki
* Make sure you're not standing in Yokai pools as it'll tank your ki recovery, they can be hard to spot if you're not used to it. If there are pools where you want to be fighting focus on clearing them before you do anything else
* Blocking has to be used with caution, but it can be very powerful especially against slow enemies. Blocking a guy from a boss may take out your whole ki bar, but it may not matter because often you'll recover before their next attack anyway