If you are subscribed to a few mods from the Steam Workshop and noticed those mods are not showing up in your game then this is what you need to do.
Go to the Prison Architect menu
Pick “Extras” from the menu
Click on “Mods” from the second menu
You will see a list of the mods you have subscribed to from Steam. Check mark each mod that you want to be active.
Then hit apply and start your game.