As i was playing on a private server that i found yesterday i came across many custom items that had chance on hits. Some of these consisted of Shape shifting into a bear, Healing yourself, and also laying a Fire totem down that does dmg to your target. I had all these weapons equipped at least once if not more and then i had equipped a Custom Axe with Regular stats no chance on hit and still had the effects.
Long Story Short Custom Weapons that have chance on hits can stack.