If you've ever been online with a hacked 3DS, assume that Nintendo has always had the ability to checked if you've been naughty. No one knows for sure, and no one but Nintendo knows what causes you to trigger an NNID ban or worse, a permanent console ID hard ban. You get logged and flagged on the server side, restoring the 3DS to stock firmware will do nothing to undo the console ID ban. If you plan to sell or give away your restored stock firmware 3DS, there is no guarantee it will or will not get banned.
Most likely not. If your sysNAND is restored to stock with no traces of GM9/Luma/B9S, you turn in a completely rewritten wiped SD card, and you make no mention of hacking the 3DS, Nintendo shouldn't have any to reason suspect hacking. You should be fine in that case. Good luck with repairs!
Edit : If you're super paranoid, after restoring the pristine stock sysNAND, update to the latest firmware, set the time & date correctly, and add a few free whatever eShop stuff. Log in some play hours if you can. Make it seem like it's been used somewhat. Or don't turn in the micro SD card.
Wrong. That option does absolutely nothing. They always log what you're running, but only when you run it while online, as proven by logging the data sent to the server. Make sure you launch a legit app before going online, since the 3DS remembers the last thing you ran and sends it to the server.
It's best to restore a pre-hack NAND backup if you have one. That ensures that the system is fully stock and no traces are left.
If you don't have one, I suggest at least formatting the system after removing CFW, as there may be traces left from previously installed CIAs. Formatting should get rid of all traces. However if you've done things like install modded system titles, region change, unban with LocalFriendCodeSeed_B/SecureInfo_A edits etc. it's not safe to uninstall CFW, and a NAND restore is your only way (or restoring everything you edited back to stock, but that's harder and if you forget something you may brick from the uninstall)
If you haven't done any of those things it should be safe.