If my opponent used Wages of Pain twice and in both instances were defied, can Ezreal's legend ability still be tapped?

Yes, your opponent can still tap their Ezreal legend ability in this scenario.

The Ruling

According to RiftJudge FAQ #473, Ezreal's legend ability triggers even if the spell is canceled (countered) after choices are made. Because the act of choosing the target occurs when the spell is played and placed on the chain, the requirement for Ezreal's ability is satisfied at the moment the spell is played, regardless of whether the spell subsequently resolves or is countered by Defy.

The Sequence

1. Playing the Spell: Your opponent plays Wages of Pain.
2. Making Choices: As part of playing the spell, they choose an enemy unit as the target. This satisfies the requirement for Ezreal's legend ability.
3. Reacting: You play Defy to counter the spell.
4. Resolution: Defy resolves and counters Wages of Pain. Even though the spell does not resolve, the choice was already made.
5. Activation: Because they have made the required choice of an enemy unit with a spell this turn, the condition for Ezreal's legend ability is met, and they may exhaust the legend to draw a card.

Note: I could not fully verify this ruling against the retrieved rules.