SQL Server Row Count sp_spaceused rows discrepancy
Yes, this can potentially affect plan choice. Does running DBCC UPDATEUSAGE make everything right again? e.g.

DBCC UPDATEUSAGE('yourdb', 'dbo.tblEMPLOYEES_MASTER'); 


Make everything right again? That doc says: 


  Reports and corrects pages and row count inaccuracies in the catalog views. These inaccuracies may cause incorrect space usage reports returned by the sp_spaceused system stored procedure.