Yes, I've seen cases where obfuscation affects performance. Remember that the JIT compiler is mostly optimised to recognize common
Java patterns and try to handle them in smart ways. If the obfuscation changes a "normal" pattern in the code to something that is not very common it may well cause the JIT to miss out on some optimisations.
As always with performance it is hard to give general advice. The best method is to measure the effects. For obfuscation this should be pretty straight forward. Measure the performance of your application with and without obfuscation and see if you can notice any performance difference.