If I configure my "McAfee Agent, General" policy to "Select repository by: Ping time", will these apply to Agent Handlers, even though I cannot configure Agent Handlers in the "Repository list" in the policy itself?
No, it won't - as you're doubtless aware AHs are not distributed repositories: instead they're able to mimic the master repository (so any machine talking to an AH that is trying to update from the master will in fact be getting its files from the AH.) Because of this the agents can't choose between AHs because as far as they're concerned they are all the same
The only way you could get round this would be to put a true distributed repository on the AH machines and use those instead of configuring the clients to update from the master. That way the clients will see multiple repositories and will be able to choose between them.