Hi 69.74.92,
It's a situation that you should try not to worry about. You are right in thinking that it's something the doctor may notice when examining you - the class 1 initial medical is very thorough, as is the two-yearly renewal. One of the things that the doctor will make note of at these examinations is any distinguishing scars or features you may have - indeed, he or she will probably ask you if you have any that they haven't noticed, so it's probably going to come up.
My advice is to be open about your scars, including how you got them (if asked). There's nothing to be embarrassed about at all, everyone has a past. Just be prepared to explain, in the same way you have here, what happened. I'm pretty sure that this sort of thing is more common than most people might think, and something that the doctor will be familiar with.
You might like to ask a question in the PPRuNe
Medical & Health forum, or do a search to see if anyone's asked before. Good luck with your application!