It's perfectly possible to discipline or even dismiss someone for suspected theft without the standard of proof you'd require for a criminal conviction. It's about balance of probability rather than beyond reasonable doubt.
Employers could even potentially dismiss more than one person for the same theft if they really cannot obtain evidence that identifies which of a small group of people is responsible.
So disciplining her without actual evidence, if it's too difficult to get actual evidence, isn't necessarily unfair, no.
However the employer should certainly be taking all reasonable steps to identify who is responsible, in the form of a proper investigation. If more money goes missing and your friend is then subject to a disciplinary procedure, a proper investigation should be part of that. If they try to give her a warning or dismiss her and as far as she can tell they haven't bothered making efforts to investigate properly, she could appeal the decision on that basis.
If there are hundreds of pounds going missing and they have any reason to believe your friend is responsible, I would expect them to have suspended her tbh. It would as you say probably be gross misconduct, meaning dismissal rather than a warning. But the idea behind gross misconduct is that the person has done something so terrible that it is impossible for them to carry on doing their job. So if they suspect her of this but are allowing her to carry on doing her job anyway, if they then try to dismiss her on gross misconduct grounds she could try arguing that they obviously didn't consider it a fundamental problem.
I think it is a fundamental problem, but it's strange they haven't suspended her, and anyone else who may be involved.