Sounds like a yucky and unlucky situation for your Dad.

However,
#1 Might be excusable, as afterall - your Dad had access to all the J lounges in HKG
#2 Three vacant seats based on what? Seat map? Seat availability? Or actual loadings?
#3 CX should have been definitely done better on this. Hotels room fully booked? Really? Do they only have one tiny motel as their partner or something??? There wass't even any huge major WX / event in town. Despite being an early flight, there should definitely be some F&B open at 4/5am at SFO.