I wish I knew how it determined what items to destroy.... if you're carrying the items on your person, you'll get a note that, say, a Boston Bugle paper was destroyed to make the Cloth you used to make a sleeping bag. While it's all "junk", there is some "junk" that I might like to use for decoration... desktop picture frames, globes, etc. I keep thinking I'm going to go into the massive junk listing in the workshop and pull out those junk items that I might want to use for decoration one day.
I'm also not 100% sure how the workbench treats weapons and armor. You can Scrap weapons and armor at their respective crafting tables, but I don't recall trying to do it fro the main workbench, nor am I sure whether the settlement will scrap weapons and armor automatically to get what it needs.
Since there's a perk that improves the results of weapon/armor scrapping, it may be independent of the workshop auto-scrapping junk. I know that you can leave Aid items in the workshop and then use them at, say, a Chemistry table (since they can be ingredients in other things). Pretty sure weapons and armor, though, cannot be accessed from workbenches at different settlements, even if connected by Supply Chains, which would suggest that they are not considered potential "ingredients" to be scrapped as needed for materials.