I personally do not believe that there is any definite proof that any code was placed in the Gateway Software that was intended for bricking consoles.
Regardless, assuming you are convinced that said proof has been found, please keep in mind that it was located by basically amateur homebrew hackers within a day of the bricks being reported.
Now take into consideration that any hacker worth his salt will tell you that by far the hardest part of hacking compiled code is finding the segment containing the instructions you wish to remove. Altering the binaries to disable the code is trivial in comparison.
If someone had the ability to locate the instruction set that bricks the 3ds when certain conditions are met within a day of the reports, he should have no trouble at all disabling that code within a few minutes by editing any one of the conditional checks to always return FALSE.
Now consider that to this date, none of the clone companies have been able to release a solution despite their claims that they have a dedicated team of professionals developing the software for their product. And instead of releasing a fix, they have had to resort to advising their customers to download a roll back in firmware which has been poorly disguised as an upgrade.
If you truly believe that multiple homebrew amateur coders have found definite proof of the intentional malicious brick code in Gateways's launcher.dat by locating the exact code, then it only stands to reason that the clone cart teams of software developers are either non-existent or so incompetent or so apathetic about fixing the issue, that they might as well be a bunch of monkeys banging away at a keyboard.
Whatever the case may be, given this scenario, the simple conclusion is that the clone cart users can not rely on the teams behind their clone carts to protect them from any malicious intent Gateway may fancy to inflict upon clone users in future updates.
In such a scenario, what would you rather trust and use? The Gateway Cart an it's team which have been proven more than competent if a bit ethically questionable or the clone carts whose teams have proven to be unable to fix in a month what amateur coders would have been able to do within a day if they so chose to.
Would you rather be safe behind the canons that may on rare occasion accidentally misfire or directly under the sights of those canons, cowering behind the paper facade of empty promises made by the clone manufacturers to protect their valued customers.