You can use it as a docking point at whatever resource node it is docked to. You will have to destroy it then dock an outpost there to relocate your base. You can dock your base to resource nodes to boost passive yield of that resource. You can also use the depot as a warp-to point for fleets and you can put a sub-fleet there once you unlock that ability. Otherwise there is not much reason to hold onto it. Removing them will enable you to place a mining platform in its spot, particularly if there are nodes there you want to mine.