Is that the one you actually made, or are those the pictures you found on other forums? I think it looks cool, and I've definitely thought about making something like this myself, but have been hesitant for the same reasons you are. My bike is an 03 so it didn't have that funnel over the filter in the first place, but it also wasn't a flat piece. The 09's stick up a few inches and were flush with the top of the airbox. I don't think there's really any issues with needing a vacuum, but where you could run into an issue is just from creating too small of a gap and restricting the airflow, not to mention if the gap is too thin the air might run in roughly, and the throttle response won't be that smooth. The way to go, if you wanted the clear cover without worrying about restricting air would be to get an 09 airbox, cut out that whole piece that holds the filter on, cut the top off flat, and then find a good glue to attach the clear piece to the top of that. It'll act as a spacer to lift up the clear piece, it'll give you a solid seal around the air filter, and as long as you glue it well enough on the top, it'll create an air tight seal where the clear meets the black plastic. Does all of that make sense?
Another option would be to cut the funnel off of a newer airbox, and attach it to the inside of your clear cover, so the rest would still be clear. The only concern there would be if it ever came loose and dropped down into the velocity stack it could vacuum seal itself, but I imagine the engine would just stall, I don't picture there being any real damage. The cool part of what you're doing though is that you could actually see the valve turning when you twist the throttle, which you couldn't do if you glued a funnel in there.
As far as your other ideas, I'd love to see how it looked painted in a mirror finish. I painted mine silver to match the frame and it makes it a lot easier to see what's going on inside the airbox cover. I thought about doing it with something more reflective, but I wasn't sure how it would turn out, plus I already had the normal silver. I love the LEDs inside the airbox if you can hide them well enough. You could look into some of the EL wire someone on here just used on a helmet, I think that looks a lot cooler than LEDs if they're gonna be somewhere you can see it.
Anyway, just for reference, here's how it looks painted normal silver to give you an idea. I don't normally leave my hose over the filter either, I usually just run it along the left side of the filter so you don't really see it. I know I have pictures of it with the cover on so you can see how it looks, but I think they're on my other computer, so I'll have to post those later.
