There is the likelihood that most encryption applications would put a header of some kind on the encrypted blob.
For example, PGP, PKZip, OpenSSL, and age all do this with encrypted files. I'm not sure I can think of a user-oriented encryption application that doesn't. Disk encryption also definitely does (although in TrueCrypt volumes the header is encrypted and not recognizable as such, so TrueCrypt is an exception, probably deliberately).
Crypto primitives in programming languages don't, and NaCl crypto secretboxes don't (they just start with the nonce!), so I guess if you were calling the NaCl secretbox encryptor by hand to encrypt your files, they wouldn't have any header.
For example, PGP, PKZip, OpenSSL, and age all do this with encrypted files. I'm not sure I can think of a user-oriented encryption application that doesn't. Disk encryption also definitely does (although in TrueCrypt volumes the header is encrypted and not recognizable as such, so TrueCrypt is an exception, probably deliberately).
Crypto primitives in programming languages don't, and NaCl crypto secretboxes don't (they just start with the nonce!), so I guess if you were calling the NaCl secretbox encryptor by hand to encrypt your files, they wouldn't have any header.