I see that it says 'Note: Projects in this bundle are hidden in your library by default until you first access them in order to avoid flooding your library. You can return to this page at any time to access any projects you wish to show in your library." Is there a way to make them all show up? I want them showing in my library

Go to your bundles (https://itch.io/my-purchases/bundles) and click on the bundle. 

Then click download on a game and it'll show in your library. 

If you want ALL the games in your library then you'll have to do this for all games.