Doesn't need knowledge, Stand dudes in general know that shit is bad, Kira himself is basically why they know that shit is bad.
Any contact with Kira or KQ will lead to Bomb#1, or even worse, contact with anything they've touched, as he can move the charge beween objects. Example, Kira can turn a button or a coin into a bomb instead, if his enemy makes any contact with it, he can use that as a intermedium, and take the transmutive charge from that object, and move it to his foe, if he thinks contact or geting to close is risky, which he would by default if Mahito can sense KQ for any reason whatsoever, as Kira would automaticaly assume he has a Stand.
He can, his bombs annihilate and vaporize the souls of those it kills. Plus it's a Stand, they can inherently effect souls and ghosts, like by default, something noted irnically while they raided his very house, fortunately Kira has a bunch of feats but even if he didn't.
Yes, he can literally transmute Stands, layered NPI, and Bomb#1 has killed ghosts flatout, and every victim's soul from bomb#1 has been shown being dusted, unable to reach heaven. All of this is on his profile. Stand NPI extends to numerous things anyway, whether it's various elemental intangibility like light and shadow, or even abstracts like WoU.
As for fear, he has a comparable will to Jotaro (this scan should be on the profile as well), he should be fine given Jotaro's will is enough that fear aura that can paralyze you, make you fear for your life, make you feel ill, all without even knowing the source, he doesn't give a rat's ass about. TW itself even has its fear hax confirmed in 6251.