The problem is that what EU4 terms "Merchant Republics", refers to what in history was City-State Republics where all power they had beyond the city itself, was based in trade within the Baltic and Mediterranean seas. Whether privilege, agreements or ports, their current power heavily relied on being able to take control of the trade within the European seas while the nobility and royalty focused on war and land.
The timeframe of EU4 covers the following aspects: trade in European seas increasingly losing relevance to the "Indian" trades. Republicanism increasingly losing to Monarchism until the French Revolution sparks a resurgence. The downfall of City States as Nation States coalesce and centralize to be able to bring more power to bear than a single city ever could hope to. Increasing mercantilism and state companies mean the Monarchist states take an active interest in their country's trade.
From a historical perspective, the only Merchant Republic that not only collapsed but actually gained power in the EU4 timeframe, was a Crowned-Republic Federation specialized in Atlantic trade, known as the Republic of Seven United Netherlands.