Unfortunately, the DoJ doesn't give a **** what pilots are paid. Obviously, even with the supposed shortage, the airlines are still paying what salaries the market will bear since pilots are still showing up for class at most places.
Though I agree with you that they won't find much of any proof of price fixing between the airlines. It is the basic law of supply and demand, combined with the fact that empty seats equal a monetary loss. Limiting the number of flights/seats, will limit the number of empty seats thus reducing loss while also reducing supply and driving up the prices. With so few airlines in the game, it doesn't take collusion for the airlines to figure out how to make economics 101 work in their favor.