For role-playing reasons, I like to keep or avoid scrapping certain junk items in my settlement for decoration or to bring out an effect (e.g. I kept the junk postboxes on the streets of Sanctuary Hills). I have also placed junk I gathered from other places to decorate my interiors (e.g. microscopes and beakers in my "science lab").
I am afraid that by assigning settlers to Scavenging Stations they might scrap those raw "junk" items I left out intentionally.
Best Answer
As stated on the Fallout 4 wikia,
So settlers will collect junk items even if none are present in the settlement and place it directly into inventory. This means that they do not pull items from your settlement.
However, if you have a large quantity of junk then there is nothing that is needed to be worried about.
EDIT: Loose non-permanent junk has a chance to despawn if the settlement hasn't been visited in a while. If you've ever had a raider attack you Will notice the bodies and items disappear after 30 days out of the settlement. There is also a chance for this to occur with dropped junk after 30 in game days.
Tl;Dr The settlers will not pick up loose junk items; however, junk items dropped have a chance to despawn after a certain amount of time.