I'm not a medical professional, but I'm guessing that the following scenario would be worse as increased exposure points exist, say if you were to change flight to be NYC-LAX (on AA) then LAX-HKG (on CX)

Considerations:

• Another airport to visit / interact with people (LAX)
• A second flight to interact with (full of people from NYC, which seems to have a virus hotspot), likely to also be fairly busy though not packed
• Risk that CX does the same cancellations or the flight is still full, so you get the two points above, plus the same busy flight and outcomes. As mentioned, these flights are down to 3 days/week now its April, so they should in theory be running with a fairly full load. I came back from SFO the week before the travel restrictions started in HKG and the flight was full in J

Personally I would consider the following, in this order:

1. Delay the flight for a few weeks if catching the virus is a real problem (shelter as garykung rightly put it)
2. Seeing what you can do about a paid/in-advance upgrade. Business class has near social distancing on Cathay anyway if you can take a "1" window seat. These are even more popular now I guess.
3. Taking the direct flight, obviously taking sensible precautions like a good mask

I honestly think that the medical/government advice is #1 (I'm no expert), unless it is a really urgent thing to get to HK. You have to balance the odds of your dad getting the virus in NYC (probably fairly low if you keep yourself locked at home), vs the chances of getting it on a 15 hour flight to HKG (which is I am guessing in the low %s, but still present, certainly the chances are you'd be exposed to it). Any pre-existing conditions or age could make that infection very serious. The only reason I'd be leaving the USA now is if I had poor quality insurance or my area didn't have ubereats/deliveroo to provide me with food when needed.