It doesn't happen all the time though? Your example is Sony patching things that are publicly known, i don't understand that -when was Nintendo alerted?
Here's how the process goes for that example.
1 - The people at HBL find a game exploit and make it into an HBL launcher.
2 - They announce which game it is.
3 - People usually have like 24 hours or something to buy the game from PSN.
4 - Sony, knowing which game it is, pulls it from the shop to check for exploits and patch it, so that once they pull it, nobody else can get that hack.
5 - Then the HBL people release the actual hack.
If they released the hack first, Sony would pull and patch the game far too quickly for any significant number of people to actually use the hack. By announcing the game beforehand but not releasing the hack or any info, they have a bit of wiggle room as it takes Sony relatively longer to find and fix the bug in the game.
In the 3DS case, only some of the bugs were fixed. Some of the internal bugs were fixed
on the system as a whole (every piece of internal software was updated according to 3Dbrew), this closed off the kernel-exploit that they were using, but not the save exploit (and ROP IIRC) they were using to run unsigned code on the 3DS in the first place in user-mode. In addition, the hackers said that there were other exploits they had that were not fixed.
If it was purposeful with knowledge of the situation, then Nintendo would have blocked the initial hacks that let people in in the first place too, like they usually do with the Wii and such. Twilight hack, smash bros exploit, etc. were fixed so people couldn't run any code in the first place. In addition Nintendo added specific checks for title IDs used by the homebrew channel and such to remove them, to further stop people from launching any sort of unsigned code.
And, while it's only one example for the DSi, the DSi had a save game exploit from an eshop game, EA's Sudoku, and it was pulled and patched after only ~200 people had exploited it. And then the DSi software was updated to specifically block copying in a hacked save for that particular game...
http://hackmii.com/2011/08/final-dsiwarehax/
So my point is that Nintendo is quite aware of save game exploits, and they can and will patch them when they know about them. But they didn't patch this one, even though the 3DS's save system has shown itself updateable (new encryption for 3DS game saves for example), and games themselves can get updates, even cart-based games like Mario Kart 3DS (got an update to fix some bugs with certain tracks). They didn't patch it because they didn't know anything about it.
Whew, hopefully that covers everything!
I'm saying is you probably don't just stumble upon and find these exact exploits unless you've been informed where to look.
You don't need to try to fix an exploit to close a hole. You just need to fix some bugs. Video game software can be buggy too, like I pointed out, and It's in Nintendo's best interest if their games/systems aren't locking up, freezing, crashing, and generally pissing off the customer. Of course, if in the normal bug fix process they do find some big thing like this...
all the better for them as far as they're concerned.
As i said i think they informed Nintendo considering they have everything working on the v4. update anyway. It's no loss at this point.
No, in fact the team tends to go out of their way to hide the exploit used from Nintendo via obfuscation, in order to make it harder for Nintendo to find the actual bug and fix it.
http://hackmii.com/2012/12/hbc-release-for-a-new-wii-u/
Despite all of the anti-reverse-engineering tricks we put into our last installment of the HackMii Installer, Nintendo managed to find the IOS exploit we used to install The Homebrew Channel and fix it sometime within the last two years.
And i don't know who you consider to be 'they' in this
Team Twiizers/fail0verflow and the individuals working on the 3DS, who are members of each others groups and/or at least collaborate depending on the association.