Because
Hydaelyn is a Primal not an actual goddess, and we now know at least one, possibly two, members of the Twelve were based on a real person from Ancient times, ala Azeyma the Warden, the goddess of the sun, is a cultural memory of the Ancient Azem, a member of the city of Amaurot's ruling council the Convocation of Fourteen, whose symbol of office was the sun, and whose soul, of course, is the player's character the Warrior of Light - reincarnated continuously throughout history to serve as Hydaelyn's protector and champion.
Azem's memory also lived on in the worship on Othard of the steppe xaela au ra clans of Azim the Dawn Father. Azem's title of office as 'the Wanderer' also apparently ended up being remembered in the Twelve, but attached to a different god of the Twelve, aka Oschon, so whether or not the other members of the Convocation also served as cultural memes of the Twelve is a very good question.
As for why Hydaelyn herself did not end up being worshipped, perhaps that was her whole point - we know worship empowers a Primal and given Hydaelyn's whole purpose was to bind Zodiark and contain him, sundering him and the original planet into the Source and it's thirteen Shards, maybe she deliberately refused worship in order to prevent herself becoming the same as her nemesis, an aether stealing abomination demanding worship, which handily explains why she is so weak, she's denying her very nature as a Primal for the benefit of the world.
But that's just my speculation.