Yes I’m sure the volume of content has some effect, possibly indexing or even Windows defender checks however I really talking about the long, long loading times some folk are getting. Just a single problematic mod might do this amongst many.
As for your situation, why not create two shortcut folders on your desktop and just drag over what you need for your flight? you can do all your browsing on bing maps/google earth beforehand … this is also a good way of vetting mods if they ever cause problems.