I think Hades' shipping of Asterius and Theseus works very nicely as a sort of metanarrative nod to the fact that the whole games was originally going to be based around people playing as Theseus to, allegedly, fight(?) the Minotaur. With this in mind it can be a cute thing, and I appreciate it.
With that out of the way, yes. Shipping Asterius with Theseus only makes the minimum amount of sense if you disregard everything else: that Asterius' sister told the secret of the labyrinth to Theseus, who in turn possibly left her to die in Naxos. And all of this happened because Athenians murdered Androgeos on the Panathenaic Games. And, later, Asterius father would die in his quest for revenge. Theseus destroyed Asterius' family irreversibly.
Minotaur Hotel's Asterion has an unique take on Theseus. One day we'll have a flashback and see what kind of person he was. I'll just say that Hades' portrayal of Theseus would make Asterion feel alienated. He fundamentally disagrees with it, so much he can't even begin to describe why.