Originally posted by Oakshield:

Junk items do disappear, however, they don't have to be in your vincinity.

It doesn't matter if you are close or not. It will despawn after a few ingame days if there is no player build structures around (workbenches, campfires, torches etc).

@OP: There is a thing you will be able to craft later that will help you to get rid of unwanted junk. I don't want to say too much to spoil it for you if you still didn't discover it.
I had one rock on the shore near my base where the sea was really deep so i threw all unwanted junk there. I actually called that Junk Deep Point :)