I never clean up mods and live very good with that. "Uncleaned" mods just overwrite records even though they don't change anything. That's usually not a problem, unless you're using another mod, which is loaded BEFORE the unclean mod and changes one of these 'dirty edit'-records, too.
Which can happen, but it's not THAT common. And you'll always see that in xEdit.
And these days, almost all mods are clean anyway. That bethesda DLCs are unclean is of no relevance, because there's NEVER any mod loaded before any of the Bethesda files, so it just CANNOT cause a problem. Period.
I wouldn't worry so much over this.