SELECT
MainTable.Nomenk as Ref,
NOM.Name as Name,
NOM.ParentRef as ParentRef,
MainTable.Serial as Serial,
SER.SerNumber as SerNumber,
SUM ((- 1 + 2 *MainTable.Income)* Number)  as Number
FROM
MainTable
LEFT JOIN
   (SELECT
     Ref,
     ParentRef,
     Name
     FROM
     Nomenk) as NOM
     ON NOM.Ref=MainTable.Nomenk
LEFT JOIN
   (SELECT
     Key,
     SerNumber
     FROM
     Serials) as SER
     ON SER.Key=MainTable.Serial
     GROUP BY Ref,SerNumber
     HAVING SUM (Number) <> 0 
     ;

SELECT * FROM (/*всё вышеперечисленное*/) as Q WHERE Q.Number <>  0