“Yup”, on the other hand, is slow, perhaps drawling. It is likely a response to an informational query and shows that you may not be totally pleased with having to answer. In some cases, it may contain sarcasm in response to an obvious question or overly inquisitive interrogator. Yes, they both mean the same thing.
In the US, in most situations of no great importance, a reply to “Thank you” with something like “Yep” or “You bet” is understood to be a friendly acknowledgement. In a situation where somebody is very thankful, especially for something that’s important to them, a greater acknowledgement would be polite.