//What happens if a person flys to/through Hong Kong these days?
Nothing. The checks are all outside
//Do you think their flight will be cancelled altogether?
Due to protests, I think the odds are low. The protesters are not dicking around with the airport now.
Also the Airport Authority has committed hari kari with the airport by imposing strict user search procedures, which has delayed passengers entering and exiting the airport
(But you're just passing thru the airport)
However, I'd be more scared that HK Airlines doesn't have the wherewithal to run this route
If your planned trip is within two months, they're good for that.
The YVR-HKG route is on the chopping board for HK Airlines though.
//Will they get a refund?
Yes, especially if you pay by credit card
But if you have other non-cancellable commitments then they are not going to reimburse you for them.