How to reference to a variable that's on a script attached to a prefab in Unity

In my game at a certain point I spawn an object and then I'm trying to get a variable from that object that I just spawned, but I get the 'NullReferenceException'.

It looks like this

using System.Collections;
using System.Collections.Generic;
using UnityEngine;

public class NewBehaviourScript1 : MonoBehaviour
{
    public GameObject ObjPrefab; //this is my prefab
    private GameObject Obj; //this is my empty object that I will spawn
    private bool isGet = false; //this bool tell me if I arledy got the script
    public ObjPrefabScript OPScript; //this is the script of the prefab

    // Use this for initialization
    void Start()
    {
        Obj = Instantiate(ObjPrefab); //here I spawn the object
    }

    // Update is called once per frame
    void Update()
    {
        if (!isGet)
        {
            OPScript = Obj.GetComponent<ObjPrefabScript>(); //now I take the script, if I haven't done that yet
            isGet = true; 
        }
        else
        {
            if (OPScript.BoolVariable) //here I'm cheking a variable from that script 
            {
                Destroy(Obj); //if it's true, I destroy the object
            }
        }
    }
}

The error is in this line:

 if (OPScript.BoolVariable) //here I'm cheking a variable from that script 

In such cases make your prefab field of the correct type right away

public ObjPrefabScript ObjPrefab;

public ObjPrefabScript OPScriptInstance;

private void Awake()
{
    OPScriptInstance = Instantiate(ObjPrefab);
}

this ensures that in the Inspector you already can only reference those objects that actually do have such component attached as a prefab. This already rules out the case that GetComponent retuns null because the component isn't there.

Further you would need to check for the existence of Obj .. you continue to call Update every frame even after the object has been destroyed.

void Update()
{
    if (OPScriptInstance && OPScriptInstance.BoolVariable)
    {
        Destroy(OPScriptInstance.gameObject);
    }
}

additionally you could also disable or even destroy this component as well since it looses its purpose after OPScriptInstance has been destroyed and is basically a wasted unnecessary Update call.

void Update()
{
    if (OPScriptInstance && OPScriptInstance.BoolVariable)
    {
        Destroy(OPScriptInstance.gameObject);
        enabled = false;
        // or even
        Destroy(this); // only destroys this component, not the GameObject it is attached to
    }
}

In general I would avoid this kind of poll checking every frame.
This component completely looses its entire purpose after the object has been destroyed anyway. So I would rather move the destroying of the object into the ObjPrefabScript itself.

Whoever is setting the flag can rather directly Destroy it right away instead without the need for any component poll checking the flag all the time.

Where you instatiate/spawn your GO, keep a reference of your newly added GO. You can access the variable by spawnedGO.GetComponent<ScriptName>().publicBoolVariable or alternatively can add a getter method for your bool variable.

The isGet = true isn't a guarantee that OPScript was loaded. It only guarantees that the program tried to grab it.

Change

isGet = true; 

to

isGet = OPScript != null; 

Also, make sure ObjPrefabScript.BoolVariable is accessible.