No. You do not need multiple certificates in order to support multiple merchants. As a developer you will need to download one certificate initially that you will register your mobile app with the wallet provider. When you add merchants to your developer account under the "Merchants" tab, a corresponding merchant token will be generated and linked to your app. You can use your certificate for any of the merchants in your "Merchants" tab.
Note- All merchants need to have an acquiring relationship with First Data.