First, why we can only kill people once ? I understood that after one it's not killing anymore but slaugthering, and that's all I understood. What happen if you kill more than one ?

It's just her family's moral code. Entirely psychological. There's no worldbuilding-specific reason for that, and thus no real consequences.

because shiki has already killed before (dark eyes guy) so it's not her first kill

I think that's because he wasn't human to her. She was fine with killing the other girl with mystic eyes as well because she has stopped being human by Shiki's moral code. I guess since the blonde guy does what he does because of love, that probably still makes him a human to her.

That said, I don't really have an explanation. You're asking for justification from the perspective of a person that defines lifeless objects as "alive".

Do we know why the glass-kun don't die ?

He probably got to the hospital in time? Don't know otherwise. Maybe the wound wasn't that bad?

Are witch common in the world ? like normal people know that it exist or is it secret.

It's kept a secret.