You are edging toward "danger" with only 16% of your Mac Storage free, but you should be OK for a while. I have seen rather crazy things go on with less than 20% free, but that is fairly rare, I think.
For more clarity: Does "scanning them into new folders in the Pictures App" mean saving your scans in folders inside your Pictures folder? And you then drag the folders into Photos, and the folder makes an Album-- is that what you're doing? That seems OK. Another good way to import pictures is to use "File>Import." Drag & Drop is not fully supported, and Drag & Drop especially gives uncertain results in exporting pictures from Photos.
You have not said what results you got from the "Referenced" Smart Album or the "Unable to Load" Smart Album.
Photos can be used two ways:
✓ Managed Library: the best, proper, and really only way that works, is to actually copy the pictures into the Library. Then you have two copies of each picture-- the one in Finder folders and the one inside the Photos Library. I move the Finder Folders to an external "archive" drive as a backup, so only the Managed pictures in the Library are on the Mac. It's a managed library because Photos knows where they are, keeps them safe, and its database can find them as it needs.
❌Referenced Library: the pictures are left in Finder folders, and Photos deals with them there. Lots of problems occur when people try this-- the database loses track of the pictures, maybe because some were moved or trashed or altered without Photos knowing about it. Referenced Libraries are handy for some sorts of testing, but never for personal use. We always recommend against a Referenced Library.
The type of Library your using is set in Photos' Settings>General:

Here you can see that I have "copy items to the Photos Library" checked. Sometimes, this changes accidentally, back and forth, so that people have some Managed pictures and some Referenced pictures. The Smart Album helps find these.
What do the Smart Albums tell you?