Yes, they will send you a confirmation email which will have a confirmation or order number and a link to your e-tickets. They asked us for our names at check in (Discovery Cove) and we brought our confirmation number just in case.
For SeaWorld/Aquatica/Busch Gardens, you will only need the eticket if you are going before your visit to Discovery Cove. If you are going after, your discovery cove pass is your ticket. If you forget your e ticket, you can bring your confirmation number to guest services and they will give you a ticket.