Don`t need Zip-archive

Is it possible to save without creating an archive? So that the files and folder structure are exactly the same as in the original?

No, Duplicati is a backup tool and not a file synchronization tool. It uses deduplication to efficiently store many backup versions. The back end data cannot be left in native format.

If you want files to remain the same, you should explore file synchronization programs.

rclone is my favorite sync tool if you need cloud support on the source or destination (or both). If you’re using Linux on both sides, rsync is fantastic. If you’re using Windows on both sides, robocopy is very good.

Very simple Backup solution has some other ideas. One interesting thing I just noticed is that Cobian Backup (a favorite of those who want the original files and folder structure, and have space for enough versions) has seemingly been reimplemented using .NET Framework (which Duplicati also uses) as Cobian Reflector. For non-Windows, FreeFileSync can sort of do versioned backups. Neither of them supports lots of remote destination types though.