Yes, there is one pool of points (based off your wisdom and Ninja level) and each activation costs one point, regardless of which power you use.
I currently have a ninja that's almost 7th level and he has not needed to use Ki Dodge, but I use Ghost Step a lot. Also, since it doesn't say "as per invisibility," he stays invisible for the entire round even when he attacks. This isn't really unbalancing, since the ninja is not a power damage character, his sudden strike is not as useful as sneak attack, he has a limited amount of uses per day, and he shares those uses with other powers.
I was sure glad I had ghost step to sneak by a roper, though!