The same list throttling limit applies to external List as in native SharePoint list (2000 items).
Instead of changing throttling limit for whole web application, we can disable list throttling for specific list (ShortUrl) via power shell. This should mitigate any issue for a SharePoint farm policy as this will not be set globally.
http://www.enjoysharepoint.com/Articles/Details/enable-or-disable-list-throttling-using-powershell-in-sharepoint-2013-21386.aspx