How Can I Make Collectable Objects?

I think you've identified how you want to do it, just do it in steps.

I would like to make that sort of thing in my game with around 100 objects

Make an array of collectables in a manager class or just a counter, depending on your needs

and when you collide with them they disappear

Make a behaviour script that destroys the game object in OnCollisionEnter or OnTriggerEnter and then attach that to a prefab.

and (For instance) it says "1 out of 100 skulls collected"

In the above collision behaviour script also send a message to or call a method on your manager (the one with the array) and either change your data array or bump the counter. Then display a message from the manager.

I would also like it if when you collect all the collectibles, you unlock a special mission or something.

In the manager script, when it receives an updated count, check the necessary requirements for a mission or something and if those are met, unlock it.

If you need help with specific scripts, post the code you have and describe how it has failed to meet your expectations, and we can try to help you out. We won't write your code for you for free. If you want your code written for you, post in the commercial or collab forums.