I noticed that MechJeb stores some vessel specific data in folder MechJeb2\Plugins\PluginData\MechJeb2\. Files have names like mechjeb_settings_type_<craft name>.cfg.

I'd like to propose to change the extension of these files from .cfg to any other value. Why? Because of all .cfg files are scanned and stored by KSP in the game database. If there is a ModuleManager installed (does anybody not install it?) then it will re-compile the whole database on any change in any config file. Depending on the number of the installed mods it may make a big difference.

Are these vessel setting files really need to be accessible via game database? Can they be a target for MM patch? If answer to the both questions is "no" then these files can safely be renamed to whatever extension that isn't recognized by KSP as database.

Files in "Plugins\PluginData" subfolders are not loaded in the GameData base by KSP. They don't impact ModuleManager cache.

Interesting. I didn't know KSP ignores configs in particular folders. Thanks for the info.

Btw, I did some more tests and it looks that having only PluginData subfolder is enough to make configs not loaded in the database.