Well, the gameplay reason would be to pace the rate of expansion as well as provide you a way to gain experience for your capitals ships (heroes). The player who can most efficiently clear the neutral ships, gain experience and pace the rate and direction of their expansion gains a tactical advantage over the player who can't. Though the player who can't (or chooses not to) may gain other advantages such as a dedicated rush fleet or intercepting your ships while otherwise engaged. 

The lore reason could be anything from pirates, neutral opportunists looking to secure loot and salvage from the wreckage of military-grade naval vessels, independent militias that try to keep the planetary population from subjugation, other parties interested in prospecting or capturing the planet and the list goes on.