It's basically because SmackDown is on UPN, and they are too scared of another thing happening with the PTC or something like that, so they try to take the easy way out, which is a big mistake.
And the reason why Austin's shirt was not censored? Look what channel RAW is on. Spike TV, and they've let RAW get away with a TON more than that. SmackDown is on networks, on which gets a TON of more heat (for some reason, the FCC lets cable get away with a HELL of a lot more than they let the broadcast networks get away with, especially after that thing concernening Janet Jackson last year, them getting scared to see another BREAST on TV again, God forbid
). I'm not surprised that the hat was censored (they censor ALOT of Cena's stuff on UPN when he would've not even gotten a thought of a push of the button if he was on RAW).