Are things like Grenades or Molotov Cocktails considered to be thrown weapons in that you can spend up to 3AP for extra damage?
They’re not listed under Throwing weapons and use explosives for attacks, so I would say no.
I would rule no, if you put extra effort into throwing a grenade, it doesn’t hit any harder (unless the grenade casing actually hits the target, and that minor bump is kind of academic compared to the earth shattering Ker-boom that does the real damage), it just goes a bit further. You are providing the force for a throwing knife or javelin, the explosion is providing the force for a grenade.
No. Partly for the narrative logical reasons that @Dom74 mentions, and partly because they’re all blast weapons where an extra die of damage translates to extra damage to several targets, so access to extra damage dice is intentionally limited.