I think it must have changed. There isn't even an 11am ferry! There is 10:45 and 11:20. They seem to run every 35 min or so on the day we are going.
This is from the website FAQ.
What does the time on my ticket mean?
The time on your ticket is for entrance to the Screening Facility for the ferry. Please line up in the Reserve ticket line prior to the time on your ticket. At the appointed time, you will be allowed to enter the Screening Facility. At Battery Park or Liberty State Park you will pass through the screening facility. After passing through screening, you will board the next available ferry to Liberty Island and Ellis Island. If you have crown tickets, we recommend you proceed directly to the information booth upon your arrival at Liberty Island.
Kris