On the current line of notebooks, it's an Apple-approved feature to run in closed-lid mode with external monitor/keyboard/mouse attached. So I'd imagine it's been well-tested and shouldn't pose any problems. (Then again, we've seen that Apple isn't perfect in quality control. But either way, you should be covered if there was a problem with it since they specifically instruct you how to do it.)
Old iBooks used to vent heat through the keyboard, but the modern machines don't.