Answering my own question, unfortunately, there doesn't appear to be a way to prevent the perfect scrollbars from initializing if pagination is disabled and the Datatable is not sized (width/height), however, one can destroy the perfect scrollbars after the Datatable is initialized using something like:

const myDatatable = new mdb.Datatable(document.getElementById('my-datatable'), myData, { pagination: false });

myDatatable._perfectScrollbar.destroy();

The mdb.Datatable object appears to have a reference to the PerfectScrollbar object in _perfectScrollbar property and calling the destroy() method on the PerfectScrollbar object eliminates the scrollbars.

Can you explain how exactly you would like it to work? Most types of datatable availible do not have vertical scrollbar so you don't experience this problem. Your point is valid only for datatable with maximum height or fixed header.