Yeah, big time. Expect to pay double or even as high as triple normal fare rates during those peak times like GW and O-bon (depending on your desitination) unless you book well in advance. Best if you could travel either right before or right after imho unless you have a pre-planned itinerary that disallows that. Then again I am referring to in-country travel so in your case coming from outside Japan it may not be so much an issue re: price hikes, not sure really.