this question should be under general ninjutsu but i will give my swing on things.
in our school we are big on using what is given to you (force, energy, space, etc). i'm not sure about aikido because i have never studied the art. anyway so if someone uses their own body force to hurt themselves then you survive another day, and don't have to do much to fight back. from what i've seen of the art there are some similar joint locks (probably because the joint can only lock so many ways). the evasion or defensive techniques from different joint locks, and attacks are probably very different.
celtic bhoy: "Are the hand techniques of ninjutsu similar to that of Aikido??"
Short answer: no.
Long answer: eh . . . sort of, but not really. Aikido certainly doesn't have the variety of strikes, and while the purpose and way of striking can be similar in some instances, e.g. open hand strike to the face to set up for a joint lock or throw.
Enson: "this question should be under general ninjutsu..."
I agree, unless celtic means specifically to compare aikido to modern ninjitsu. Maybe a mod or admin can move it over?
I have trained in aikido for three years, so could offer more, but since I'm not an expert on the modern styles, I'll refrain for now while this topic is in this forum.