Does Countersquall counter a spell that has already had its effect replaced by a replacement effect?

Countersquall counters a target noncreature, nonland spell. Countering a spell means it is removed from the stack without resolving (CR 701.5a). The key point is that countering and replacement effects operate at entirely different moments in the game.

Replacement effects (CR 614.1) modify how an event occurs as it would happen — they don't apply to spells sitting on the stack. A replacement effect that would change what a spell does only becomes relevant when that spell actually tries to resolve and produce its effect. If the spell is countered before it resolves, it never reaches that point, so no replacement effect tied to that spell's resolution ever applies.

There is a narrow related concept: some replacement effects apply to the spell being countered itself (e.g., 'If this spell would be countered, exile it instead'). These are replacement effects on the countering event, not on the spell's effect. Countersquall can still target such a spell; the replacement effect just changes what happens to the spell afterward (CR 614.1c).

Concrete example: Your opponent casts Isochron Scepter's imprinted instant. Suppose a replacement effect would change what the copy does upon resolution. You cast Countersquall targeting that spell. The spell is countered and removed from the stack before it resolves — the replacement effect on its resolution never triggers, and you gain 2 life from Countersquall regardless.

In summary, Countersquall targets and counters the spell on the stack. Replacement effects that would alter the spell's resolution effect are irrelevant because the spell never resolves. Only replacement effects that specifically modify the countering event itself would interact with Countersquall's action.