For the record, you mention "the limitations of the number of inodes in Unix-like systems", but this is not a limit in Unix, but a limit in filesystem formats (which also extends to Windows and other systems).

So it depends more on what the filesystem is rather than the OS. A FAT32 partition can only hold 65,535 files (2^16), but both ext4 and NTFS can have up to 4,294,967,295 (2^32). If using Btrfs then it jumps to 18,446,744,073,709,551,615 (2^64).

I know, I read it because I wanted to know too know if it was addressed

Well I'd you have so many data entry, yaml and toml are not that helpful either. They would present different sets of problems. You should use a database (perhaps sqlite) for that purpose.