The "jailbreaks" now have access to both processors used to boot the system and games, so they can run code before the system loads and intercept writes to their memory locations.
They can block exploits in new firmware versions (and have), but the system has sold so many units there doesn't seem to be a realistic chance of "breakable" systems running out for those interested.
As long as you don't install some theoretical update that blocked all the exploits directly onto your real NAND, or as long as you don't buy a fresh 3DS with this update baked in already... you're honestly all set.
This shifted later on in the console's lifetime, but at that point people had already developed "backup loaders" and most users were already in for the piracy more than the homebrew.
Not that homebrew isn't great, but it would be a complete lie to say piracy isn't the biggest application of these exploits.
Say what you will about the piracy scene, but Nintendo almost killed it with the newest software updates. It took passion and experience, not money, to cause the newest events of what happened here. What if that passion could have been redirected into cool homebrew in the first place?
On a sidenote, do companies in general want to allow home brew on game consoles? Especially if they're selling them at a loss or at break-even, since they're not going to make money if people buy the consoles just for homebrew purposes.
This culture of "homebrew" truly blossomed during the DS era with a huge number of commercially produced rewriteable cartridges, and 3DS piracy is largely a continuation of that.
The PS3 had this issue when the US Air Force built a super computer out of them a while back[1], since you could run Linux on the original PS3 without a jailbreak. They latter pushed an update that disable this feature in response.
[1]: http://phys.org/news/2010-12-air-playstation-3s-supercompute...
The PS3 supported installing Linux onto it and there were people internally supporting it.
Yellow Dog Linux was the officialish distro: https://en.wikipedia.org/wiki/Yellow_Dog_Linux
What's more likely is that once Geohot and others started hacking the machine, sometimes through linux. Someone at Sony must have realised that it's an attack vector that a miniscule amount of users used.
And it'd be better for them to get rid of the functionality.
> And it'd be better for them to get rid of the functionality.
On the other hand: The people who love to hack Linux to run on their toaster are often the people who have the knowledge to exploit the device. As long as Linux already ran from beginning on, this kind of people had no real incentive to attack the device to run Linux. As soon as this option was removed, this kind of community got furious on Sony and decided to let their exploits loose.
Nintendo generally seem to be very anti-homebrew/community lately, using the DMCA to shut down fan projects seems to be their way of destroying that reputation that they built over the 90s.