That's why when Eric Clapton and Greg Allman took the covers off from their LP's pickups experienced significant amount of tone improvements. Countless other famous artist did the same thing. Even Page and Beck did the same after seeing Clapton do this.
Nowadays, modern covered humbuckers don't suffer anymore from high end loss because of the quality and type of non-conductor material used on making the covers ( German Nickel ). I, personally prefer covered humbuckers simply because to me, they give my Les Pauls more of the Vintage appeal. Specially now that the covers are made 100 times better than the old ones and does not affect tone anymore.