Q. Can someone detect that a file has messages encoded in it?
A. If the file was generated with an encoder whose code is public (i.e. Github, bitbucket, ...) then yes. Always. And even if the code is private, it may not be secure. Unless you come up with an encoding scheme that's never been thought of before, then law enforcement will likely be able to detect the encoded messages unless they're trivially short.
I have been working on a new steganography algorithm that I believe is secure. I plan to make it open source in the new year. Would you like to review the design and code when it is released?
Q. Can someone detect that a file has messages encoded in it?
A. If the file was generated with an encoder whose code is public (i.e. Github, bitbucket, ...) then yes. Always. And even if the code is private, it may not be secure. Unless you come up with an encoding scheme that's never been thought of before, then law enforcement will likely be able to detect the encoded messages unless they're trivially short.