The NSA will still have everyone's fingerprints
That and if you were ever booked as part of an arrest, did military service, held a high level security clearance or applied for a drivers license in some states, the data is already there.
Now the question is, yes someone may find "your" fingerprints somewhere but that is not conclusive proof that you were there.
For the last twenty years, silicone materials and masking techniques have been around where you can easily lift a fingerprint off almost any smooth surface and apply it to a silicone material surface to make a counterfeit fingerprint impression. The cost of these materials is less than $20 and can be picked up at any good chemical or rubber supply shop.
I can see the DefCon seminar now, "How to spoof the iPhone 5S with Counterfeit Fingerprinting"
The basic techniques are out there on the 'net already.