I'd go with separate tables here (if you stick to WP-Table Reloaded, more on this in a moment).
WP-Table Reloaded was not really designed for large tables (like thousands of rows), and you might see a drop in performance - and what's even worse, a drop in usability. For example, the "Edit" screen for such a large table will probably be rather useless, and either slow or not loading at all. Import of such large tables could work, but it can also be troublesome.
So, for best efficiency, I would leave the tables separate in WP-Table Reloaded.
Now, however, for what you describe, one large table might indeed be better. Instead of using WP-Table Reloaded for it, you might however want to explore the possibility of some custom PHP code to access a custom mySQL table with your data.
This should then also give you more advanced search possibilities in that data. You could of course also use the search from the DataTables library on that table manually (see http://www.datatables.net). But as that would also require loading the entire table, this could in theory become slow. A custom search in mySQL would probably be the fastest then.