No. The wonders are still disabled in the M2TW game. But their effects are still workable in M2TW.

Statue of Zeus at Olympia
population_loyalty_bonus bonus 4

Colossus of Rhodes
trade_base_income_bonus bonus 4

Pyramid of Giza's effect:
population_loyalty_bonus bonus 3 requires factions { egypt, }

Temple of Artemis at Ephesus
construction_cost_bonus_other bonus 30

Mausoleum of Halicarnassus
construction_time_bonus_other bonus 20

Pharos of Alexandria (I am not sure for his effects on naval units)
Effect HitPoints 2
Effect MovementPoints 4

Hanging Gardens of Babylon
farming_level 2