1. Seal looks legit, the box looks fantastic. If you show us more pictures of where the openings are on the box it might help a bit more.
2. Most people I think go for the box protectors. I got my protectors for N64 stuff from
http://www.videogameboxprotectors.com and I'm really happy with them. Obviously if you have it graded it will be well protected.
3. As others have mentioned, my first guess was that it is a vent hole. I wouldn't worry about it honestly. Obviously don't put stress on the hole, but it should be fine.
4. Totally up to you. Figure the price of shipping and the specific grading you are going after, then see if it's worth it to keep it in its current condition. If you have other games graded then it might be good just to have a collection going. If this is your first sealed game you are considering getting graded, maybe collect a few more and see if this route is something you want to follow.
Congrats on the find, it looks really nice!