Repeatedly creating/recycling axes and swords would go through multiple item handles. You would be better off saving, then go through a batch of crafting and reload if you don't get a reasonable percentage with +AP bonuses.
It would be better to delay crafting if you don't need the items or gold.
Local items in the world (some pre-placed items) are not assigned a global handle if you do not pick them up.
I don't think pickpocketing or killing an NPC creates a new item handle.
Avoiding containers that tend to have less useful contents will help a little bit, but I'm not sure how significant that would be overall. It would probably help more not to check every merchant every hour, if you didn't actually need equipment upgrades or new skills.
I think each item in a chain of crafting does require a handle, but I'm not sure about items added to an existing stack.
The 1.06 update was for a separate, PS4-only issue, unrelated to the item handle limit (though the symptoms were similar).
