Why was it such a disadvantage to have such a small fleet of merchant ships?
It is difficult to answer this question well without more of a context for it; without knowing when and where the question refers to.
In general, having a small fleet of merchant ships would have been seen as a disadvantage because it would have made it harder to be in control of one’s own trade. For a long time, countries believed in the idea of mercantilism. They believed exporting more than one imported was the only way to wealth and power. When such beliefs dominate, it will be important to have a large merchant fleet. A large merchant fleet allows for more exports and it allows a country to export without having to depend on any other country.
In this view, having a small fleet would make a country dependent on other countries and thereby put it at a disadvantage.