Within Qlik Replicate add an option for Gathering Stats on a table after a full load is issued (either the initial load or reload). Issuing a truncate command clears the table statistics making the use of the table non-performant. Normal database maintenance functions manage the incremental processing but there is a delay between full loads and the maintenance procedures. Having the tool perform the Gather Stats would close that gap and keep the database performance within expectations.
A good place to add this setting would be in the Task Settings, Full Load Settings.