If the target spell is an illegal target by the time Draining Whelk's ability tries to resolve, the spell doesn't resolve. You don't put any counters on Draining Whelk. If the target is legal but the spell can't be countered, you do put counters on Draining Whelk.

For spells with {X} in their mana costs, use the value chosen for X to determine the spell's mana value.

Draining Whelk's ability counters the target spell even if you can't put counters on Draining Whelk, most likely because Draining Whelk left the battlefield before the ability resolved.