If Cunning Nightbonder enters the battlefield while a spell with flash that you cast is on the stack, that spell can't be countered, even though you don't get the discount.

Cunning Nightbonder's cost reduction applies only to generic mana in a spell's cost. It can't reduce a spell's colored mana requirements. For example, your first Cunning Nightbonder won't normally reduce the cost of your second since it has no generic mana in its cost.

Cunning Nightbonder's last ability doesn't apply to itself while it's a spell.

Players can't attempt to remove Cunning Nightbonder to raise the cost of a spell you wish to cast, but they can remove it to allow their spells and abilities to counter your spells.

To determine the total cost of a spell, start with the mana cost or alternative cost you're paying, add any cost increases, then apply any cost reductions (such as that of Cunning Nightbonder). The mana value of the spell remains unchanged, no matter what the total cost to cast it was.

A spell or ability that counters spells can still target spells with flash you cast. When that spell or ability resolves, your spell won't be countered, but any additional effects of the countering spell or ability will still happen.

Spells with flash that you control but didn't cast (perhaps because they're copies of a spell or because you took control of them from another player) can be countered.