This is a good remark. I don't love project_db.dat either for various reasons. Sometimes it is complicated to keep it in sync with the actual files, for example when you copy resources from another project. It is also a source of conflicts when several people create different maps/sprites/etc in the same project at the same time.
Still, it is useful to maintain a list of resources. In some of my games, I have .lua files inside the map folder that are not maps but scripts that maps can call (but okay, there is no .dat file with it in that case so the auto-detection could work).
Also, I wouldn't like to have to browse subdirectories recursively to find resources. The engine would need to do so, as well as the editor and various tool scripts like data files converters.
project_db.dat also gives a user-friendly name to each resource. However, now that maps and tilesets are identified by strings instead of integers, this is not so important as before.
So, to conclude, I have mixed feelings about project_db.dat. I might remove it in the future, yes.
Now in your use case, you can add maps dynamically into the savegame directory and forget to add them to project_db.dat. These maps will work in the engine, but not in the editor and other tools. Which is not the ideal solution, I agree.