I'm not an EE so don't take my word for granted...
That said, are you hardwiring your pumps or plugging into an outlet controlled by an SSR? If you are plugging into an outlet just install a GFI circuit to cover your pumps. As for your 12v control bus, fuses are not a bad idea, but you need to have a handle on the amount of amperage you will be drawing through it before you select the appropriate fuse. What other devices are you planning on running on here? Can you get either a watt rating or amperage draw of your 12v equipment?