How interesting - have never taken a look at the back end of the machine - I shall have a look at an MD95 (B717 ? .. .. passing fad) tail end in a week or so when the opportunity arises.
As you observe, a VG on the 717's engine nacelle clearly is not very relevant to the wing airflow .. but will, nonetheless, be a flow control device.
One needs to keep in mind that such devices are a means of getting around a flow problem - usually an undesired separation - and can appear, in appropropriate shapes and sizes - in many and varied parts of an aircraft.
I would expect that the intent, in this instance, is to delay nacelle flow separation's blanking of the lower rudder -which is relevant to aft cg stall (and spin) recovery considerations.