For me the aspects of reuse, flexibility and compartmentalising of functionality far outweighs any organisational issues that might be apparent within the Shortcuts app. I still find that in Shortcuts itself, anything over fifty lends itself more efficiently to searching.
However, I would note that a good naming standards/hygiene is incredibly useful in regards to searching and organising, and if you are having organisational issues or feel you could, then you should absolutely be considering LaunchCuts (episode 45).
If you happen to have naming standards and LaunchCuts, you can even use Smart Folders to great effect in automatically organising many of your shortcuts.