It will NOT cause a sealing problem qith the filter.
Back in June 2011 during the first dyno session with my Vaquero i completely cut out the smaller circular area of the emblem on the left side air box lid and LOST 5 h.p. due to the air "choking" as it tried to pass thru the connector channel between the 2 air boxes. During the dyno run i could feel the air coming OUT of the hole due to intake reversion. I did a couple of runs to make sure of the accuracy, and sure enuff there was a MAJOR loss of power. I then did 3 more runs, first run taping off 1/3 of the hole, power went up, 2nd run taping off 2/3 of the hole, power came up again but still below the best run with an un-cut a/box lid. then the 3rd run with the hole completly taped shut, power back to stock.
If you are gonna cut a design into that area the back side of the air box lid would have to be sealed so no air can go thru the design you have cut .I have done this on skoots before and glued chrome or carbon fibre pattern material on the inside, you can even use a piece of material in a color to contrast and compliment your skoot.
The extra air that a replacement k&n filter supplies to the engine does not cause the air to "choke", if you want more air thus more power it will have to be accomplished with a Big Air Kit.