Not all MC breeders do--some specifically try to breed for it. My recollection is that the trait was not that rare in original Maine MCs. I think if you google "maine coon polydactyl" (without the quotes around your search) you will find lots of links to MC-specific info, including breeders.
You are correct they're are breeder that specifically try to bred polydactlys , but in CFA and TICA shows it's cause for disqualification.
Seems to be common with orange tabbies, we had a big friendly neighborhood cat we called Ole Six Toes.
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