Logic tells me clearing your log could also get you ban potentially. If your log was uploaded to Nintendo when using your switch Unmodified, and they happen to keep logs of your logs, then next next you go online it upload your blank log = you modified your console = breaking user agreement = ban right...?
If you use Hekate and dReport, it clears the logs on Boot so that shouldn't be as much of an issue. As far as I understand, it only submits the logs when something crashes - so if you delete the log on boot when nothing can crash, it should (in theory) clear any signs of CFW or modding.