It saves a lot of money just using PDF's from their regular production. Most of the magazines who have switched over to using HTML/CSS look pretty good on the iPad. But re-doing every issue in HTML is a pain and a lot of work. You can include a retina PDF, but it makes for a huge file size, so its hard to win.
I run an iPad travel magazine and we ran into the problem of our images just not being big enough. Not every travel writer carries an SLR, one carried an old point-and-shoot and the images were like 720 pixels wide! We couldn't even go full screen on the regular iPad.
So yeah, its not as easy as you think to figure things out, especially if you're designing for both dimensions, then you need even bigger images.