Assuming the story is true then acknowledging it would be more damaging that denying it (and they may have been directed to deny).

Remember also all the denials regarding PRISM.

If this is being correctly handled by the intelligence services (and you can have your doubts on that following these leaks) then nothing further will come out anyway.

For what it's worth, the Register mentions that Apple suddenly dropped Supermicro as a supplier.

The bottom line is that those denials don't really contribute much information.