According to the FAQ, "Non Combat Damage is always applied as soon as it is assigned before any other actions can be taken."

Does it mean that Non Combat Damage is not affected by Toughness ?

No, toughness is not an action. You don't activate it. It is always on, so would still protect the unit.

Not to mention tat Toughness, like all cancel effects takes place during the damage application process.

And the Forced of the warrior priests of the empire?

Forced effects trigger WHENEVER their conditions are met.