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).
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.