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Seeker of Secrets, page 43, "[Ioun stones] have no effect on animals, mindless constructs, and other non-sentient creatures."
PFS FAQ reads:
"'Can I improve my companion’s Intelligence to 3 or higher and give it weapon feats?No. An Intelligence of 3 does not grant animals sentience, the ability to use weapons or tools, speak a language (though they may understand one with a rank in Linguistics; this does not grant literacy), or activate magic devices. Also note that raising an animal companion’s Intelligence to 3 or higher does not eliminate the need to make Handle Animal checks to direct its actions; even semi-intelligent animals still act like animals unless trained not to. An animal with Intelligence of 3 or higher remains a creature of the animal type unless its type is specifically changed by another ability. An animal may learn 3 additional tricks per point of Intelligence above 2.'"
So it appears that familiars [outsiders and magical beasts] can use Ioun stones, animal companions cannot.
Quoted from the previously mentioned posts. It looks like the fact that his mount is a magical beast allows it to use them...