Neither of Kopala's abilities will increase the cost of spells or abilities that target only Aquitect's Will, even though it's a Merfolk spell. They work only if (among other things) the spell or ability targets a "Merfolk" you control, which means only a Merfolk you control on the battlefield, not a "Merfolk spell" on the stack (C.R. 111.1), or a Merfolk card elsewhere than the stack or battlefield (C.R. 109.2).
No. An Aquitect's Will on the stack isn't a merfolk you control; it's a merfolk spell you control, an important distinction. Spells on the stack, permanents on the battlefield, and cards everywhere else are all mutually exclusive categories, and anything that singles out a card type/subytpe without saying "spell" or "card" only ever refers to permanents by default. Kopala, Warden of Waves only protects merfolk permanents, not spells on the stack.
Got a question about interaction between Aquitect's Will and Kopala, Warden of Waves.
IIRC - any spell on the stack is under it's caster control - does this mean that any spell (for example some kind of "counter target spell" effect) targeting Aquitect's Will while I have Kopala in play will cost 2 more?