It
shouldn't, depending on the sampler you use. The sampler normally will resample on the fly. Where it can cause problems is that there is some overhead in doing this, and I've experienced a few buggy samplers that will work correctly during a session, then the samples are played at the wrong sample rate when you open the project later.
This is pretty common though. I record at 24/96 and many of the sample libraries I use are 16/44 and Sonar handles it without issues.
Regards,
Dan