I don't know.....I think every bike I've ever torn down had mud caked in the seal area/ trapped by the boot or gaiter.

I think if you'll take the time to keep the tubes/seal area clean and maybe after washes blow the water that pools there off.....not only would it likely be as good, it'd probably extend tube/seal life over putting boots/gaiters on there and forgetting about it...............

Hell either way it's not big deal; use your judgement/do what you want.....it's not like it's gonna cause a wreck or blow an engine.