Specialized worrying about small shops is certainly ironic. They definitely have been one of the players central at pushing out the small shops. They were one of the first pushing concept stores and are really squeezing the margins of small shops.
It's been an interesting observation to see how all the big brands have been massively increasing their margins through cheap manufacturing in China (a frame that costs >$4000 retail is less than $300 for those guys to get to the US) while the margins are incredibly low for the actual shops (<10% often) especially on high end bikes. I know many shops now make their primary income on bike servicing.
I think specialized avoiding amazon is more a case that they don't want to stay the big guy that can push the small shops around, instead having to deal with the 500lb gorilla that amazon is.