Entity Reference field fails when choosing from more than 1000 items
I haven't tested whether Oracle's performance with Entity Reference is substantively worse than another backend such as MySQL.

However, implementing the workaround detailed here and converting a Drupal user.module query to a dynamic form to also implement partitioning worked, albeit with a 50 second execution time and a hugely increased PHP memory requirement. This is because of multiple complex queries across the whole node set.

Switching to use of the references module and the node_reference content type has vastly improved performance.