So this isn't an option in the game. You can scrap guns at a weapon workshop, armor at an armor workshop, but you cant scrap junk at your base workshop. I strongly dislike having a cluttered "Junk" category. I've been dropping all of my junk items and scrapping them upon every time i return to base. It isnt that bad, theres something kind of nice about doing this, but i've probably wasted a lot of time doing this and it would be much easier for an option to scrap individual items in your base/building workshop or even have items automatically get scrapped upon storing into your workshop. (I can see people opposing this due to accidentally scrapping a junk item that they would want to keep as that item, like jangles the moon monkey).
* * * pro tip
for the people like me that are dropping and scrapping, use the flat bases for houses as the platform you will drop them on. I'm talking about the places like at sanctuary where you can scrap an entire 'ruined house' and nothing is left but a perfectly flat base. This prevents items from going slightly under a layer of ground. in other words, you can always see EVERYTHING you dropped.
dont forget a single pencil. lead is your friend.