Sometimes you don't want particular clients to see any standard reports (or maybe forms), but if you delete the standard plugins folder, MoneyWorks will recreate it on next launch.
You can delete the subfolders and leave the Standard Plugins Checksum file in place: this will prevent MoneyWorks from reinstalling the folder until at least the next software update.
To permanently prevent standard plugins recreation, delete the content you do not want (say, the Reports folder), and create an empty file in the Standard Plugins folder named No Standard Plugins (you could just rename the checksum file to this). If this file is present, MoneyWorks will not reinstall standard plugins.