Strange... I'm using the version from the Nolf revival site and I can play the game and the bonus missions with this patch installed.
Check pcgamingwiki, maybe they have a solution.
Viewing post in No One Lives Forever 1 - Modernizer comments
You should check your startup.txt file, sounds like the file nolfgoty.rez could be missing from there. This is the file that contains the extra missions.
This is the order it should load in:
[Rez]
Rez0 = "nolf"
Rez1 = "nolf.rez"
Rez2 = "nolf2.rez"
Rez3 = "nolfdll.rez"
Rez4 = "nolfl.rez"
Rez5 = "nolfu003.rez"
Rez6 = "nolfc001.rez"
Rez7 = "nolfc002.rez"
Rez8 = "nolfgoty.rez"
Rez9 = "Custom\MODERNIZER.REZ"
Note: if you're using Nolf revival version you should rename or remove WidescreenGOTY.rez from your game folder. Their version of Nolf.exe has instructions to load this file coded into it. This may override some files in Modernizer.