Polymorphy effects do not remove the polymorphed creatures's languages, they only prevent using them if the form acquired does not support speaking (chicken fits that). I cannot find any rule that reduced Intelligence should void the presence of racial languages, nor those learned by spending ranks in Linguistics (though arguably it might temporarily remove skills gained because of high Intelligence bonus), though again it reduces or prevents meaningful communication.
The eidolon rules says that it speaks all the summoner's languages (which summoner still has, though is not able to use them), not "all the languages the summoner can currently speak" so I would assume that the eidolon still can speak and communicate meaningfully.