Thanks to Harry458 for finally recognising the essence of and motive behind my post. I was beginning to think that there was some kind of campaign to discredit me and to suspect who might want to do that ...
It's good to know that there are some travel agents out there who realise that the client should come first!
To be honest, I had the same thoughts as the mojorob and bex76 at first. We see that kind of post all the time here, so it's certainly not a stretch of the imagination.
Regardless of that, I checked out the site and am somewhat surprised sites like this still exist. The key point here is never give out credit card details just to get availability information. All reliable hotel booking websites don't operate this way so it's totally unnecessary.
Looking at a page like this one I'm actually inclined to think this site is borderline fraud. Look at that list of facilities. Then look underneath it. Those facilities actually aren't there, they are just listed in that clear fashion so you think they are. It's pretty dodgy really.
There's a bigger take away here and I think we'll see that a lot in the coming years. Once you've found a reliable site to book with, stick with them if you can and if they have competitive prices. More and more sites are going to pop up that are just scams to get credit card details. They'll be way better thought through than this one too and really the customer has no way of telling unless they know the company behind it is reputable. It also happens to be why I think meta search for travel isn't going to be all that fantastic. Trust is still a big part of any booking (offline too, but especially online!).
Anyway, I guess you won't be making that mistake ever again!
Sam I Am, I am grateful to you too for your clear insight and articulate analysis.
JapanHotel.Net certainly does not seem to be putting its clients' interests first. It appears to be a small, couple-run enterprise and I understand their need to make money. This apparently means that they can never compromise or make concessions. Lucky I hadn't booked for a month! 100% penalty may be their policy, but does anyone believe the hotel couldn't or in fact didn't let out my room on the second night, once I hadn't shown up for the first? I trust they're happy with their neat profit.
No, I certainly won't ever make the same mistake again, and I hope no one else will either.