As another commenter said, if your table have required ID columns, you should specify it in your SELECT.

     SELECT x.Id,x.a,y.ID,y.b 
     FROM x 
     LEFT JOIN y 
       on x.a = y.a    

The output [Id12345,5,Id6789,NULL] means the column is null. The output [Id12345,5,NULL,NULL] means the row is empty.

On a side not, I use the SQL below all the time to identify missing rows on the "comparetable".

  SELECT #basetable.columnname
  FROM #basetable
  LEFT OUTER JOIN #comparetable
  ON #basetable.columnname1 = #comparetable.columnname1
    and #basetable.columnname2 = #comparetable.columnname2
    and #basetable.columnname3 = #comparetable.columnname3
  WHERE #comparetable.columnname1 is null