In datatables 1.13.11 it was done via height: 0px, that the duplicated header is visually hidden.
But screenreaders and users using the tab key on the keyboard can still reach this duplicated and visually hidden header.

Normally you use aria-hidden="true" to exclude these from screenreaders.
Additionally you have to remove it from the keyboard navigation via tabindex="-1".

In the current datatables v2 the same problem exists, but the code is different.
You can easily test this via the following steps:

• install NVDA from https://www.nvaccess.org/ and run it
• go to https://datatables.net/examples/basic_init/scroll_y.html
• click into the Search input to focus it
• press tab key 6 times
• now press tab key once, you are now in the hidden header and get the first column name (NVDA will read aloud "Name" header column)

Relevant code in 1.13.11:
https://github.com/DataTables/DataTablesSrc/blob/1.13.11/js/core/core.scrolling.js#L313

There are probably more instances (like footer and so on), where visually hidden elements are reachable via tab key and are read aloud via screenreaders (NVDA).