It's not that clearing your browsing history, throwing out old logs/emails or flushing your toilet are inherently illegal, it's when you use them and why.
Exactly; it's analogous to shredding documents. People shred documents all the time. If you do it as a matter of course (e.g. because of document retention policies, or just because you periodically clean and shred stuff you don't think you want anymore), you're not doing anything wrong.
But if the FBI asks you some investigative questions about something and then you immediately go shred a bunch of stuff, they're going to argue that you were doing that in order to destroy evidence. Intent matters. A lot.
Same thing here: if you're using incognito mode or routinely clearing history and cookies, there's no issue. If you do it in response to an investigation, they're going to argue you did it to destroy evidence. Intent matters.