Update: Thomas at Bootswatch says changing the link tag contents is the best way to change themes on the fly. EG in this post: New App Design Considerations - Part 8 BS4 Themes Sample Project
I would also look at this post on DataTables forum for the dark mode issues, there is very little posted about dark themes and datatables: Datatables styling issues with bootstrap (White background in black themes) — DataTables forums
However, Thomas has suggested adding these CSS definitions, which works nicely on initial testing:
div.dts div.dataTables_scrollBody {
background: none;
}
.table-striped tbody tr:nth-of-type(odd) {
background-color: rgba(0, 0, 0, 0.05);
}