I have some personal photos inside
/home/my_username/Photos

and family photos inside
/home/shared/Photos

I want to manage both of the above.
Digikam, however, wants to mix everything into the Album I have defined (which is /home/my_username/Photos).
The project seems mature, so I don't think it's a bug, but rather a feature.

But why??
It's so obvious that people may store photos in various location, so what's the reasoning behind this behavior?

Have you added each as a seperate collection in Digikam > Settings > Configure Digikam > Collections.