If you do a search, a few weeks back someone posted a pic of a K&N filter mounted on top of the airbox, that seems like it would work well for when the hood is off.
FYI, a cold air intake can just as easily (easier actually) be used as an underhood intake, all you have to do is not add the venting & leave it open to the hood area. You can do this with any of the standard intakes, cutler, bdx, D&D, timbersled... it's ALL in the install.
If you just don't want the open style intake & want to keep the box, that is the best solution that I've seen so far.