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For simplicity sake alone I would say No. As long as services don't share infrastructure (eg. a database) you shouldn't mix them so you have an easier time updating your scripts.
Another point is handling stacks. When you create dockers via compose you are not supposed to touch them individually. Collecting them all, or even just in categories, muddies that concept, since you have unrelated services grouped in a single stack and would need to update/up/down/... them all even if you just needed that for a single one.
Lastly networks. Usually you'd add networks to your stacks to isolate their respective Backend into closed networks, with only the exposing container (eg. a web frontend) being in the publicly available network to increase security and avoid side effects.
So right now I have a single compose file with a file structure like this:
Would you in that case use a structure like the following?
Or a different folder structure?
The second one is exactly what I have. One folder for each service containing it's compose file and all persistent data belonging to that stack(unless it's something like your media files)
The second is exactly how I do it. Keeps everything separate so easy to move individual services to another host if needed. Easy to restart a single service without taking them all down. Keeps everything neat and organized (IMO).