1. Is it fair to find both Bob and James guilty of the crime of theft?

Yes, that's right.  The applicable principle is that, if the material facts of two cases cannot be distinguished, both cases should be decided in the same way.

In the example, the materials facts are the same for both Bob and James. Both were in possession of the stolen property taken from the house, and both of their fingerprints were found in the house.  Neither of them could satisfactorily explain these matters.  On these facts, it is fair to convict both Bob and James of theft.