Yeah, the Bubble Bobble 2 cover we have right now was actually made from a label scan I took from my cart a few years back, which is why the art is slightly cut off on the sides! Pretty sweet to have scans now. The stickers can definitely be worked around with a bit of effort.
I'd be very cautious removing the stickers though if you decide to do so. Be 110% patient when removing them, and you should be ok. I've certainly removed stickers in worse situations with fantastic results, but this is Bubble Bobble 2. The one on the front doesn't look like it would be too much trouble, but the sticker on the back looks like it might be a little more risky. But really, considering where it is it doesn't really need to be removed anyway. Those parts can easily be restored regardless.
If bg_gamer is just making this cover with the new NES template, I'd absolutely love to update our current cover as well as create a true retail cover to match.