Why not use a block placer (deployer I wanna say?) to place missiles after fired. Or maybe that new advanced color coded deployer set to put up a specific missile when you power a certain wire color. One silo, many types of missile with no additional footprint!
I ended up using deployers for the "magazine" system. They were be kept underground and cycled up to launch position where upon deploying a missile it would automatically wire in to a targeting controller. After launch the deployers got fed into a block breaker so they could be used again.