If NoteCaddy is disabled then it shouldn't be starting at all so please report this to us with your log file:
Tutorial: Reporting A Problem
In the meantime if NoteCaddy is still starting when disabled then you can manually disable it as follows:
1. In PokerTracker 4 select the 'File -> Open User Data Folder' menu item.
2. Go into the 'Apps' folder.
3. Go into the 'Tm90ZUNhZGR5' folder.
4. Rename the 'NoteCaddyPT4.exe' file to something else e.g. '_NoteCaddyPT4.exe'.
5. Restart PokerTracker 4 and NoteCaddy will no longer load.