Yeah, that can be frustrating. but you shouldn't have that problem. I don't know if cuteFTP offers recursive delete or not (check your help file) but if not, you might want to consider a more full featured FTP client. If your FTP client supports recursive deleting, you will be back to a single delete command on DH.
Sure you can! That's a function of your FTP client, not DreamHost. For how to set up CuteFTP to display hidden files,
The DH Wiki has instructions. So does Google, or once again, check the CuteFTP help.
It can sometimes take a little time to get adjusted to how things work differently at a different host; once you find your away around your FTP application, and DreamHost in general, you'll likely never be happy with the "G*D*ddy way of doing things again (DH is much more flexible and powerful from the users' perspective).