The point is: we can show stuff on the screen if we want, even if the application is using a raw framebuffer. And a screen is superior to leds to show information.
Which isn't always helpfull, especially with the screen beeing off. I often use my Pandora in USB-Mass storage mode, with the screen automatically turning off after a while. How should I see wether I left WiFi, Bluetooth, 3G on or wether there is SD-activity or not ?.
What if I want to use the Pyra in the dock ? Why do I need to inconveniently search for status in a taskbar, applet, whatever, If I could have all the info I need by just looking at a certain area of the Pyra ?.
And this isn't a big problem if use the "middle ground" some here already brought forward: 3 RGB and three single color leds. This way you can have your fancy christmas tree (which I would not want in a device I use in public, the flickering probably drawing my attention away from the screen, and with a pattern I probably need weeks to memorize) and "we" can have something that is conveniently usable, easy to understand, not cumbersome to use and won't cost ED a lot more (some traces and two additional holes I guess).
But leaving, were to put them as a problem - I would still prefer a place were they can be seen independtly from the lid status. I personally would prefer the Thinkpad way - in the display lid (lower part) with a hole on both sides and transparent overlays over it (
http://support.lenovo.com/en_US/diagnose-and-fix/detail.page?DocID=HT003713) or like Acer did (does?) on some models, with the LEDs beeing visible "over the edge"
(http://commons.wikimedia.org/wiki/File:Bluetooth_Logo_on_notebook_(with_LED).jpg).
But both options don't seem very probable though (due to costs and mechanical/wiring problems).