And seriously, there was risk when using custom firmware on any console, why it wouldn't be the same with the 3ds? even if they are selling their work on the discovered exploit, it's still custom code.
Also, they are not working for nintendo, they didn't built the system so even if they added a code breaking console... it's must likely not the problem here. It's more likely there's something different in the last fw from nintendo and when you're using emunand, the gateway code break new check or code from nintendo which brick the console.
If gateway can brick your console, nintendo can do the same. They add a check on the last firmware, to look for gateway code and bam bricked... or their last firmware try to update some low system on console... and bam bricked because gateway code was interfering...
Anyway, a big part of the scene is hidden, we don't even know what's been discovered about 3ds os... no syscall, no systeme function, no kernel function... NOTHING! So how the hell do you expect thing to got that well out of the box??? Like how the hell it's can be possible to update the emunand without a once of fear from nintendo new code?