And why is it at Lv. 1?
First of all, I would say that there is no definite anwser because it's Gamefreaks decision to do this. But I have a few reasons that could also help.
If you add all of my reasons above together, you will find out that Mat Block was the right choice of signature move for Greninja. There is no definite reason for this so these are based on my opinion. And also, signature moves are usually gotten at level 1, thus making it special.
Assuming you are referring to Water Shuriken, all of the Kalos starters have a move like that. Greninja has Water Shuriken, Delphox has Mystical Fire, and Chestnaught has Spiky Shield.
The level 1 thing is simply to allow you to use a Heart Scale to remind them of the move should you choose not to teach it to them. They will immediately be given the chance to learn it on evolving.