What could cause a clunking noise when hitting a bump in a Honda Pilot 2019?

When vehicle hits bumps in the road, a clunking/thumping noise happens. Sounds like spare tire is hitting but actually it's, because that has been checked and is secured tightly. Very annoying.

Perhaps it's one of your CV joints. They tend to clunk when they are worn out.

Considering it's a 2019, take it back to Honda and let them check it. If they say they can't find anything wrong, take the service advisor and/or technician for a ride on a rough road to demonstrate your concern.

Could be something askew in the suspension, could simply be the exhaust hitting the bodywork. Try getting underneath and wiggling the exhaust to see if you can replicate the noise. If it's that, it's usually easily rectified by adjusting the way the exhaust hangs or by replacing missing hangers.

Could be a loose or damaged suspension part.

Aside from the exhaust bumping into something (I agree that's probably the most likely cause), have you hit any big potholes or really big bumps with it while at speed at all? I ask because a broken spring can also make a clunking noise when hitting bumps. If you can pinpoint that the sound is coming from one particular corner of the vehicle, I'd take a good long look (or have the dealer's shop look) at the condition of the spring at that corner. It's fairly easy to miss seeing a broken spring if you're not looking specifically for it and it's even possible that a manufacturing defect etc., caused the broken spring even if you don't recall hitting any huge bumps.

Bad ball joints
Bad stabilizer links or bushings.
Possible bad struts.

It's under Warranty, but if you want to find out quicker take it to a Tire Shop and ask them to check the front end. Tell them it clunks over bumps. They'll do it free and you won't have to wait long… Like at the Dealer.

Don't mess with it. Might void the warranty. Let the dealer figure it out.