Currently, the only way to do so is by editing the FormID Lists* (for individual objects) or the COBJ records** (for "types" of objects), easiest way would be with FO4Edit. There is a plan to make it changeable in-game, but that will require additional development of F4SE and someone to recreate the Mod Configuration Menu.

For editing it yourself, it's pretty easy to find the relevant record:
1) In-game, open the console and click on the thing you want to make unscrappable***
2) Launch FO4Edit (I recommend deselecting all plugins but the SE plugins)
3) Search that FormID. This will give you the placed reference. 
4) Under that record, there will be a "NAME - Base" subrecord. Hold Ctrl and click on that. It will take you to the base object
4a) The base object is the item listed in the scraplist and is the one that needs to be removed. 
5) Select the "Referenced by" tab at the bottom, if you only launched this mods plugins there should only be one record. If not, select the one with the FLST signature showing as being in SE's plugin. Double clicking that record will open it.
6a) If you want to just remove that item, just locate it in the list of records, and delete it. 
6b) If you want to remove the whole category, select the "Referenced by" tab for the FLST record, and open the COBJ record associated with it.
7b) Delete the value in the CNAM field

*delete the object you don't want scrappable from the record

**delete the CNAM field from the relevant record, or delete the record itself. I recommend just deleting the CNAM, since you could more eaisly "re-enable" it for scrapping by adding it back in. With the way the records are named, it'd be pretty easy to tell. 

***sometimes you'll select a "mist" record, which is essentially the floating dust effect you see in places. Just click around till you get the right thing, or "disable" the dust, it's not very noticeable most of the time, and if you accidentally disable the object, you just have to "enable" the record before clicking on something else (or you lose the record id, and have no way of finding it without reloading an old game or figuring out which placed reference it is by looking at the cell in the CK or FO4Edit)