• Just like czl I do have seperate apps for each type of data I use. For example Ente for photos and Syncthing for keeping the documents folder of my devices synced up.
• It’s not something I really think about because my data sources are functionally disjoint. (e.g. I don’t have photos from my phone in my documents folder). The only exception is Ente, where I do keep a plaintext copy of the “shared with family” account to display some family photos on our digital photoframe. This also “answers” your next question.
• I don’t have anything set up for when an application stops support. I do however do look beforehand whether it’s possible to extract my data in a way I can migrate to another platform if need be. For example, some services like Ente offer an easy plaintext way to export/backup your data in directories mirroring your albums. That way I could easily head to Immich
• It hasn’t really. I usually do backups by keeping two copies of all my volumes. So running more services doesn’t really impact much of anything.

A sidenote on Nextcloud: it does use the same folder structure in its data volume as it presents to the user. So it’s fairly easy to manage, but you need to update the folder you made the change within the container for it to show up. When we used to keep photo’s synced up with Nextcloud, I could directly access that folder for the photoframe. Since Ente is e2ee I needed to duplicate data in that case