Easy way to find out if it's your sample libraries that are causing the long load time: freeze all of your sampled instruments, save the project, close SONAR and re-open the project. Most of the time, the difference will be dramatic. It's not about having Kontakt in your project per se, but rather what libraries it's having to load.
Given the extreme load times you're experiencing, though, the plugin-scan theory is the more likely explanation. There is really no reason to do the scan on every startup. It's only enabled by default to simplify new installations for new users.