Melafix and Pimafix actually spent years being tested on fish under controlled condiitons. I have spoken to the scientists who developed them. They are considerably more effective than not treating, and are not simply an aid to healing. They even have some advantages over antibiotics (aside from the issue of harming the biological filtration, there is better wound healing and much lower incidence of secondary infections when these treatments are used). I have tried to ask the scientists which is better - Melafix or antibiotics - but they won't be drawn, because they say there are too many variables.
It is true to say that API do not know which bacteria/fungi these treatments work on, because they have not been evaluated this way. They were tested on living fish with infections, not on bacteria/fungi in petri dishes. The active ingredients in Melaleuca or Pimenta have not all been identified by science, and it is impossible to know exactly how they work. However, evidence from API's tests suggests that, as well as anti-bacterial or anti-fungal action, these plant extracts may have anti-inflammatory and immunostimulant activity as well.
However, you must never try to make up your own treatments using, for example, Tea Tree oil from the chemist. Firstly, this is not the same type of Tea Tree oil as is in Melafix/Bettafix (different species of Melaleuca), and secondly, without an emulsifier it will not mix with the water properly. Not only will this mean it is ineffective, it could actually be harmful, by forming a film over the water.
