Hiya, long time no see!
I don’t use any programs to do my organising, so perhaps someone who does can advise you there.
But, I too have loads of music files and pics etc on my external drive, and the way I do it is this:
For pics, I create one main folder (call it what you like - mine is called “My Pics” - original eh?). Inside this, I organise the pics into more folders - “Holiday 1999”, “Christmas 2009” etc.
For the music files, I organise the the files into folders by artist, then inside those, Album folders.
Can take a it of gruntwork starting it all off (I remember organising my mum’s external HDD once - took forever!), but it’s fairly easy to maintain once you get into the routine of backing stuff up at the end of the day/week/month/decade.
There are probably decent freeware apps that’ll do the work for you, but I’m awkward and always take the long route round anything.
For duplicates, I find (if I don’t discover them during organising) Quintessential Media Player (free) can search them out and remove extra ones. Other media players do this as well I would think.