I have different apps on the same machine and I wan to backup their databases and some assets.
Is it better to use one repository for all or rather one repository for each app? Or even one for each kind?
What are advantages/disadvantages of those variants?
These are extremely broad questions. It depends on your use cases, needs and requirements. This has already been asked here and there, have you done any searching to find information about it?
Relevant aspects are deduplication, retention policies, security, and it also depends on what backend you intend to use (e.g. if you use rest-server you can use --append-only).
I’m using a mounted & encrypted S3 storage and if I interpret this correctly, it is rather recommended to use separate repositories.
With append-only I will lose the ability to forget and prune, right?
Depends on your needs and use case 
From the client backing up, yes. You can still do it on the server where you run rest-server or from whatever system that has access to the repository without --append-only.