People brick their 3DSes by attempting to use Gateway mode with a DSTwo+ "emulating" the GW card.
It doesn't brick 100% of the time, every time, some people have tried to brick on purpose but never managed to. Nonetheless, unless you have a DSTwo+ and plan on running GW then you don't have to worry about that.
The other way people brick, which may be more relevant to your situation, is by updating via sysupdater while in rxMode sysnand instead of
devmode/pasta mode (or updating sysnand while in GW mode.)
If you have the right firmware update pack, install a cia manager to sysnand (rxTools has an option to inject FBI directly into the Health and Safety app) and install sysupdater, then you can go in the rxTools menu and load devmode/pasta mode.
devmode is only present in 2.5.2 and 3.0 nightlies (newer versions of the nightlies changed it to "pasta mode" but they are the same thing.)
They call it Pasta Mode because PastaCFW was a cfw that ran on sysnand and originally was pretty much just sig patches with no firmlaunches. rxTools was merged with PastaCFW, so devmode was eventually renamed to pasta mode because it pretty much is exactly like running the original PastaCFW.
Basically you need devmode/pasta mode, because it is only sig patches and no firmlaunch. Firmlaunch is what causes a brick when using sysupdater, because it loads a newer NATIVE_FIRM in memory which confuses sysupdater into thinking a newer NATIVE_FIRM is already installed.
As a result, it doesn't update NATIVE_FIRM and you are left with a sysnand that won't boot and is pretty much useless unless you can get a hardmod and restore a nand backup.
rxTools devmode isn't the only option, if you can run PastaCFW w/o firmlaunch that also works, or PBT-CFW (very outdated so better not to bother.)
rxTools is the best choice since you,ll already be setting up and using rxTools, so why not use what you already have
If you're going to be using a 3.0 nightly, I recommend the 9/28 nightly.