Here's a very late response:
Key issues are load times and Google rankings. One of the issues is that the content that is "above the fold" (using the newspaper term) must load very quickly or you'll take a rankings hit. This means that all the content that will fit in a browser window when first landing on a page should be up within a second or two. The closer to instantaneous the better. When figuring out where the fold is, you have to make allowances for people with high resolution monitors and still have room to spare.
All of your cool, resource-heavy content needs to be below the fold and loading in the background while the visitor is taking in the above-the-fold content.
Another issue is with menus. A drop-down menu requires a much larger live area than the menu bar itself so you may have to create separate drop-downs for each main menu item and have them jump in and out of the window so you don't have a huge area that blocks interaction with the content below the menu bar.
The best solution for me has been to create the shell of the site using a dedicated page design app, to have the Hype content on separate layers and to keep the resource-heavy stuff down the page, and to do the menus in the web design app. When creating a vertically scrolling page, I prefer to create an inline layout that alternates vertically between blocks of Hype content and blocks of content designed in the web app. Sometimes I will have a tiny Hype element integrated into the block of web app content (such as a small slide show of detail photos or a cool series of animated button-sized Hype animations with the button actions set by the web app.