CFW + CIAs alone - No bans
Cheating - Maybe (especially if you cheat in free-to-start or free-to-play games like Nintendo Badge Arcade)
FlahsCards - Yes if you use public ROM dumps without altering their headers to a private one, or specially Sky3DS if you rely on their standard template.
If you patch the ROMs to use private headers (that is, a header dump that only you have access to) then you're safe.
People seem wary of using tickets files to get content from Nintendo's servers with homebrews like FBI, tikdevil, freeshop and others but I dunno how those processes actually work so I can't confirm anything about these matters.