Unisci la tabella 1 alla tua query aggregata come sottoquery.
SELECT t1.name, t1.apn, t1.bpn, t1.code, t2.*
FROM table_1 AS t1
JOIN (
SELECT APN, count(APN) AS APN_count, min(aCost) AS min_aCost, min(bCost) AS min_bCost, ceil(avg(aQty)) AS avgQty,
max(aQty) AS maxQty, sum(bShipped) AS sum_bShipped,
CONCAT(truncate((avg(aResale)-avg(aCost))/avg(aResale),2) * 100,'%') AS avg_Margin FROM
(SELECT name, APN, BPN, aCost, aQty, code
FROM table_1
WHERE customer = '12345' AND
aDate >= '2013-01-01' and
aDate <= '2015-12-12') as qh
INNER JOIN (SELECT CPN, bCost, bResale, bShipped from table_2
WHERE customer = '12345') as ih
ON qh.APN = ih.CPN
WHERE bShipped > 0
GROUP BY qh.APN) AS t2
ON t1.APN = t2.APN
