It says "per level", not "per ninja level". Is this intended, or typo.
it impacts rouges taking
Ninja Trick (Ex): A rogue with this talent can choose a trick from the ninja trick list. The rogue can choose but cannot use talents that require ki points, unless she has a ki pool. A rogue can pick this talent more than once.
examples
Ki Pool (Ex): A rogue with this talent gains a small ki pool. This ki pool is similar to a ninja's ki pool, but the rogue's ki pool does not grant any extra attacks. The rogue gains a number of ki points equal to her Wisdom modifier (minimum 1). These ki points replenish at the start of each day. If she already has a ki pool, or gains a ki pool later, she gains half her Wisdom bonus (minimum 1) as bonus ki points to her ki pool. She can spend a ki point to gain a +10-foot bonus to movement until the end of her turn.
Vanishing Trick (Su): As a swift action, the ninja can disappear for 1 round per level. This ability functions as invisibility. Using this ability uses up 1 ki point.
Ventriloquism (Su): As a swift action, the ninja can throw her voice as if using the spell ventriloquism. She can use this ability for 1 minute per ninja level. Each use of this ability uses up 1 ki point.
From the "Classes" section of the core book under "Multi-classing":
Note that there are a number of effects and prerequisites that rely on a character's level or Hit Dice. Such effects are always based on the total number of levels or Hit Dice a character possesses, not just those from one class. The exception to this is class abilities, most of which are based on the total number of class levels that a character possesses of that particular class.
So for a class ability, when in doubt "level" means "class level".
Having said that, I'd rule that a rogue using Ninja Trick should be able to use his/her rogue levels instead of ninja levels for whichever trick he/ahe picks, but YMMV.