I know this is going to sound silly with someone with not even 10 posts correcting someone with nearly 18,000, but I figure I should at least make this clear for the benefit of some random people who may happen to read that comment and misinterpret it.
AFAIK, Nintendo would have to put in a change on the bootrom hardware level - in other words, practically design a new 3DS SoC - in order to fix this. So it's not something that can really be "dealt" with by Nintendo - at least, unless Nintendo can "deal" with it in the same sense that one can deal with a tornado, hurricane, or earthquake.
It's too late in the 3DS lifecycle for that, and we all know that within a few years they will wind down the 3DS and move on to the Switch as their main system. 3DS at this point is destined for maybe one more year of decent support, and then the slow death of shovelware/kid games that the DS got.
I'm sure once the New2DS XL comes out, it will be Boot9Strappable, since they're already no doubt being manufactured, meaning that they'd have the same exploitable bootchain. The issue there will be getting a hax running to install B9S - if we're lucky, it might be a low 11.X firmware (and thus, Soundhax), but if it's 11.4 and up, right now the only way to do that is hardmods or System Transfer - and the latter is a potentially dubious prospect.
So basically now, Nintendo is more going to rely on that there is a (rather good!) number of people who either won't learn about Boot9Strap, won't want to proceed with it, or fear the negative misinformation and scary warranty voiding that installing it does to their systems.
They'll still make decent coin.