No. Luma3DS has FIRM protect on by default, so it'll always keep FIRM0/FIRM1 from being updated by Nintendo. So you can update just fine. I've gone from 10.7 to 11.0 just fine, and that was when 11.0 was the new thing. If running Luma3DS it's impossible for you to install stock firmware. You have to go out of your way to remove it yourself, by using Decryp9 to flash back a clean sysNAND backup that doesn't have A9LH.
This is why we setup Hourglass9, as that always keeps A9LH, so you never have to worry about losing it if you don't remember if a NAND backup has A9LH. Or if you simply forget to use the (keep a9lh) option in Decrypt9. Before Hourglass9 was a thing, I would see a couple posts of people flashing a NAND without A9LH without using the keep a9lh option, and then complaining that they spent hours for nothing, when it was clearly their fault for not choosing the correct option in Decrypt9.
Now I'm kinda nervous that I chose the right options..... how can I double-check before I update?
Oh.... and two last things.... so, which files are absolutely necessary to keep so I can continue to boot my N3DS after all these hacks are installed? I have a LOT of un-needed junk now and would prefer to get rid of all this extra stuff I no longer need all over my card.
And.. after I fully update it, do I need to do anything special to perform a system transfer from a fully updated but unhacked 3DS... or can I just perform one as if neither of them were hacked?