Somebody will correct me if I'm wrong, but there is no difference as it pertains to jailbreaking. That being said, I'd say why not -- move to iOS 6.1. There isn't anything spectacular about iOS 6.1, but I'm sure there are a number of bug fixes that are packed in.
If you update, it's recommended that you do so via iTunes and not OTA.
An OTA update has potential for causing it problems with the jailbreak and the SHSHs are different, which may prevent you from being able to restore to 6.1 after 6.1.1 is released. These are things that may not matter in the future, but it's better to be safe than sorry. I always avoid OTA updates just to play it safe.Why is an OTA update not recommended?