Yes, you can emulate a device disconnect by removing VBUS. This will work 100% with VBUS-powered devices like pen drives. The situation might be somewhat different if the device is self-powered. There are badly designed USB devices who might ignore VBUS and maintain functionality of serial interface. As a matter of fact, power cycling is the only way to force device disconnect (in embedded situations you usually can't mechanically remove the device). When VBUS is removed, the device UFP must turn off HS termination and remove D+ pullup.
Your second proposition will also work provided that each pen drive is connected to a different USB port. But if you plan to use all pen drives on the same data lines, data signal integrity will be compromised, and you will likely suffer from unstable functionality.