My 04 came with that mod as well. I taped over it when I did the H2W jetting and pre-filter kit install. (Which was a drastic improvement on my bike's overall performance, highly recommended!)
Over the Texas summer the tape came off and the bike would backfire on decel (a problem that had gone away after install of the H2W kit).
If you go with the pre-filter and jetting kit you might replace the cover, or seal the hole, as it may affect some of the carb circuits by changing reference pressure in the airbox. That's my best, unproven, guess at the relationship between that hole and the decel backfiring.
On another note, should your bike have a Facet fuel pump, or, you find the need to replace the OEM, be sure to get the Facet model that blocks fuel flow when it is shut off. A previous owner of my bike seemingly installed the one that allows fuel to flow through, even when not pumping. This has led to two instances of gravity feeding fuel into the engine when a float valve didn't close. Now, I just turn the petcock off at every stop until I replace the pump.
I'm sure you will get lots of good input from the OC during your makeover. Best wishes for a rapid completion.