I have a view that the amount of extinguishing agent provided by the manufacturer per "shot" will be based on the volume of space inside the engine cowlings. This volume can only take so much extinguishing agent. If you discharge both together, a significant amount will be forced outside the engine compartment and lost. If you fire one shot and then wait a period of time (and 30 seconds seems the standard), you will have the full quantity of the second shot left if the fire is not fully extinguished by the first shot, minimising the amount of agent lost outside the cowling.
Having said that, if the manufacturer's Flight Manual instructs you to fire both together, you should do so unless you have good reason not to.