at 9 means 9 pm which was the bedtime of the kids at the orphange and if u remember at the end of the manga u had a ninja talking about it aswell and also talking about kabuto, kabuto has been wondering who he is and where he belongs.
It also happens to be a very unlucky number for Japanese people and is a homophone for suffering. 4 is also unlucky and is a homophone for death. They also believe that if you catch a crows eyes something awful will happen.