Calcular Días Presente y Ausente de la tabla

Puede intentar la siguiente consulta:

SELECT e.comp_mkey, e.status,   e.resig_date,   dt_of_leave,    e.emp_name,
   e.date_of_joining,  e.emp_card_no,   a.pl_days,    pl_days_opening,    a.month1,
   a.month2,   a.month3,   a.month4,   a.month5,   a.month6,   a.month7,   a.month8,
   a.month9,   a.month10,   a.month11,   a.month12,       
   a.month1 + a.month2 + a.month3 + a.month4 + a.month5 + a.month6 +   a.month7 + a.month8 + a.month9 + +a.month10 + a.month11 + a.month12 AS pl_sum,
   m.[DaysAbsent],m.[DaysPresent]
  FROM p_leave_allocation AS a
   INNER JOIN
   emp_mst AS e
   ON a.emp_card_no = e.emp_card_no
   INNER JOIN
   (
   SELECT 
        comp_mkey,emp_mkey,[month],[year], 
        SUM(CASE WHEN data ='AB' THEN 1 ELSE 0 END) AS [DaysAbsent],
        SUM(CASE WHEN data ='P' THEN 1 ELSE 0 END) AS [DaysPresent]
    FROM
        (
        SELECT comp_mkey,emp_mkey,[month],[year],[Day1],[Day2],[Day3],[Day4],[Day5]
        --,...  
        FROM Emp_mon_day
        ) source
        UNPIVOT
        (
        data FOR day IN ([Day1],[Day2],[Day3],[Day4],[Day5]) -- dynamic query can generate all days data
        )up
        GROUP BY comp_mkey, emp_mkey,[month],[year]
   ) AS m
   ON m.comp_mkey=e.Comp_mkey and m.emp_mkey=e.mkey
   --- ABOVE CRITERIA NEEDS TO BE CHECKED
  WHERE  a.year = 2016
   AND (datediff(MONTH, e.date_of_joining, CONVERT (DATETIME, getdate(), 103)) >= 6
        AND datediff(MONTH, e.date_of_joining, CONVERT (DATETIME, getdate(), 103)) <= 36)
   AND (e.resig_date IS NULL
        OR (e.dt_of_leave IS NOT NULL
            AND e.dt_of_leave >= CONVERT (DATETIME, getdate(), 103)))
   AND e.status IN ('A', 'S')
   AND e.comp_mkey IN (7, 110)
   AND a.Year = 2016;

Explicación:

Agregamos otro INNER JOIN a la consulta existente para obtener datos recopilados de DaysPresent y DaysAbsent

Para optimizar esto aún más, le sugiero que aplique directamente siguiendo WHERE cláusula a source establecer

WHERE  comp_mkey IN (7, 110) AND Year = 2016;