You must use object pooling for the projectiles.

In a nutshell it instantiate all the bullets when the scene loads, and then it reuses those GameObjets over and over again without the need to instantiate new ones.

Here is the code I wrote to tackle such issue:

ObjectPooling.cs (Attach it to an empty GameObject):

using UnityEngine;
using System.Collections;

public class ObjectPooling : MonoBehaviour
{
 public GameObject prefab;
 public int poolSize;

 private GameObject[] pool;

 void Start ()
 {
 pool = new GameObject[poolSize];

 for (int i = 0; i < poolSize; i++) {
 pool[i] = (GameObject)Instantiate (prefab, transform.position, Quaternion.identity);
 pool[i].SetActiveRecursively (false);
 }
 }

 public GameObject RetrieveInstance ()
 {
 foreach (GameObject go in pool) {
 if (!go.active) {
 go.SetActiveRecursively(true);
 return go;
 } 
 }

 return null;
 }

 public void DevolveInstance (GameObject go)
 {
 go.SetActiveRecursively (false);
 }
}

SpawnPool.cs (Attach it to a GameObject that will spawn the bullets, in your case the ship or soldier holding the gun):

using UnityEngine;
using System.Collections;

public class SpawnPool : MonoBehaviour
{
 private ObjectPooling pool;
 private GameObject go;
 private int contador = 2;

 void Start ()
 {
 pool = GameObject.FindGameObjectWithTag ("BulletPool").GetComponent<ObjectPooling> ();
 }

 void Update ()
 {
 //Debug.Log(contador);
 //contador++;

 //if (contador > 2) {
 go = pool.RetrieveInstance ();

 if (go) {
 go.transform.position = transform.position;
 }

 // contador = 0;
 //}
 }
}

AutoDevolvePool.cs (Attach it to a bullet Prefab):

using UnityEngine;
using System.Collections;

public class AutoDevolvePool : MonoBehaviour
{
 public int time = 2;

 private float seconds = 0;
 private ObjectPooling pooling;

 void Start ()
 {
 pooling = GameObject.FindGameObjectWithTag ("BulletPool").GetComponent<ObjectPooling> ();
 }

 void Update ()
 {
 seconds += Time.deltaTime;

 if (seconds >= time) {
 //Debug.Log("devolvido");
 pooling.DevolveInstance (gameObject);
 seconds = 0;
 }
 }
}

Hope that helps!