Ninjas do not natively have any way to spend ki at 1st level. However, there are some benefits to having ki even if you cannot spend it. In addition to the +2 bonus to Will gained for having at least one ki left, having a ki pool is a requirement for a number of feats in Complete Scoundrel:
- Enduring Ki
- Expanded Ki Pool
- Ascetic Stalker
- Elemental Stalker (Dragon vol. 357, not Complete Scoundrel)
- Martial Stalker
- One with Earth and Water (Dragon vol. 351, not Complete Scoundrel)
- Zen Fortitude (Dragon vol. 351, not Complete Scoundrel)
The first two don’t do anything without something to spend ki on, but you can take them as a 1st-level ninja when otherwise you might have to wait until 3rd. And Ascetic or Martial Stalker could actually do some stuff for you even if you are a 1st-level ninja—for instance, if you are also a 4th-level fighter, Martial Stalker would add +1 to your AC bonus, and if you are a 7th-level monk, Ascetic Stalker increases your unarmed strike damage by one die size (hey, I didn’t say these were good just that they are literally not nothing). Elemental Stalker is similar. And then Zen Fortitude is actually kinda good (Wis instead of Con on Fort saves).
There are also a (very few) feats that allow you to spend ki, and could be taken by a 1st-level ninja:
- Karmic Healing (Dragon vol. 351)—spend ki to heal yourself a tiny amount.
- Wolf’s Bite (Dragon vol. 351)—spend ki to temporarily get Improved Feint, Improved Disarm, and Improved Trip.