Has there ever been a dub with honorifics in it? I'm not too familiar with English dubs.
These dubs include some, but not necessarily all honorifics:
Ai yori aoshi + Enishi
I My Me Strawberry Eggs
Angelic Layer
Please Twins
Planetes
Welcome to the NHK
Samurai 7
Basilisk
Azumanga Daioh
Ouran High School Host Club
Lucky Star (maybe, can't remember)
A lot of the time, they'll retain some of the most crucial or emblematic honorifics for a series, while dropping the rest. Like they use "Chiyo-chan" in Azumanga, but omit most others.
As for Clannad, the dub director (Steven Foster) is known for liberal and not-so-faithful dubs. These range from outright gag dubs like Super Milk-chan and Ghost Stories to controversially re-written dubs like Generator Gawl and Orphen. But those last two are from ~10 years ago, and it all depends on who's doing the actual scriptwriting. *checks ANN* Turns out Foster's only directing/writing the first 12 episodes; there's a different director and writer on 13-24.