I would expect most heritage railways are operating as a Registered Charity (or other form of incorporation with charitable objectives approved by the Charity Commission). If so, then they can include a power to create and enforce Byelaws for he regulation of persons and activities on their property. There is no reason why 'fare evasion' could not be one of them.
But if you are asking if the 2002 Railway Byelaws, which regulate activity on the UK mainlines, has been applied to heritage railways, then no. That would not be possible. (Although I can't determine whether or not anyone has attempted to prosecute a breach on a heritage railway).
. . . . . I know that trespass has been prosecuted, but that was by the police working alongside a railway, not the railway prosecuting directly.
Yes, and many other offences, such as theft, vandalism and safety, but these are not Railway Byelaw offences.