It depends on the complexity of the business logic you want to implement.
let's take an example here, if I were in the business of putting a home buying escrow onto the blockchain, I would make each deal it's own contract (even though the terms of different deals may be similar). If I were building a lottery contract that executed every day, I would put a master contract for all lotteries on the blockchain. In another example, if I were to build a gambling business that supported multiple game types, I may have one master contract that tracks all activity and then delegates to a game specific contract.
So, basically it depends on the business logic. But surely we can have a master contract linked with other contracts if your business logic demands.