Shows all GameObjects in the scene with hideFlags, so you can debug them.

HideFlagsUtility.cs

using UnityEngine;
using UnityEditor;

public static class HideFlagsUtility
{
    [MenuItem("Help/Hide Flags/Show All Objects")]
    private static void ShowAll()
    {
        var allGameObjects = Object.FindObjectsOfType<GameObject>(true);
        foreach (var go in allGameObjects)
        {
            switch (go.hideFlags)
            {
                case HideFlags.HideAndDontSave:
                    go.hideFlags = HideFlags.DontSave;
                    break;
                case HideFlags.HideInHierarchy:
                case HideFlags.HideInInspector:
                    go.hideFlags = HideFlags.None;
                    break;
            }
        }
    }
}

I've been working around editor scripts and I've come across with object hiding at some point. However they've managed to stay hidden out of my control. This script helped me a lot, so thank you!

Thanks for sharing. I would like to make some minor additions;
Sometimes objects are staying disabled, that's why i used var allGameObjects = Object.FindObjectsOfType<GameObject>(true);

Also i needed to search for null components: int nullComponents = go.GetComponents(typeof(Component)).ToList().FindAll((x)=>x is null).Count;
of course, to use ToList() and FindAll() , you also need to add using System.Linq;

i hope these also can help for someone if needed.

This is excellent, thank you! I had a couple of hidden prefab objects in my scene that had broken references, and since they were hidden, I could never see them in the hierarchy. This worked perfectly to show them and let me delete them. Thank you! :)