Hey Ray, thank you for you answer!
I have been investigating about any changes that could have been implemented by a third party but got nothing.
Also, I tried to reply this behavior on a "empty" standard DB which gave me the same results that the one I am using.
As far as I can see you can keep stock (shown as stock on hand but not available to sell) by sending it to a scrap location while it's value is turned to $0 (if the location type is inventory loss). I tried to make an inventory adjusment but got a pop up saying: "Editing quantities in an Inventory Adjustment location is forbidden,those locations are used as counterpart when correcting the quantities."
So, this behaviour is a bit confusing as I understand it's a good tool to keep scrap in stock somewere in the system but not as stock on hand.
If you have any other comment it would be much appreciated!

I would suggest you log a ticket with Odoo Support. I just tried it again and when I sent one quantity to the out of the box "Virtual Locations/Your Company: Scrap" location, one quantity was removed from Quantity on Hand (9 units became 8 units), but if I clicked the Smart Button and removed the "On Hand" filter and used the "Positive Stock" filter instead I could see the same quantity in stock as was shown after the scrap (8 units) plus the item I sent to the Scrap location (1 unit) for a total of 9 units.