A note is a comment that is added to the ticket by the agent. An agent can choose to add either a public note or a private note to a ticket. The public notes will be visible to the requester when they’re viewing the ticket on the portal, whereas private notes would be visible only to agents who have access to the ticket.
A reply is an email communication that is sent out to the requester’s mail address. The replies sent by agents would be visible on the portal for the requester and also be sent directly to the mailbox of the requester.