That's a possibility but I cannot confirm it's 100% safe though. Also don't forget a NAND backup before doing anything homebrew related in case something makes the Switch crash.
NX-deport doesn't delete all crash (error) reports AFAIK and it even got some people banned.
I'm just telling you to grab a NAND backup prior to doing your operations on the clean Switch.
I've had Checkpoint crash on my second Switch the first time I used it that's why (hopefully I had a NAND backup).
If you use Atmosphere you won't have to worry about the error/crash reports, because it redirects them to the SD card so they don't get saved on your system