His reputation is unlikely to take a hit. Each case is unique and it's never really as clear cut as win or lose. Simon Jordan says we lost the UEFA case with CAS remember! I would expect the calmness within City (based on the rumours) to be because Pannick has advised on each and every charge and its chance of success/failure. He'll have advised them on how to manage the process with the PL from day 1. He knows how to argue a point, which case law to rely upon, which words to use and all the tricks in the book which is why he costs so much.
The failure to cooperate is going to hit us. I can't see how it wouldn't. Similarly to CAS, you have to cooperate with a sporting body in order for it to carry out its duty. We'll have arguments around why we didn't, but I would expect us to get short shrift and be fined. Again, I'd anticipate Pannick has a fair amount of evidence to justify why we didn't cooperate and, if it gets to the sanction stage, why it should be a financial and not sporting penalty.
Being cleared of all charges is a 6-0 win over the rags.
Being cleared of all but the non-cooperation and getting a fine is a 6-1 win. You celebrate both the same!