IGh
This what I "know".
The vortex generators were there on the 737-200 - I know because I saw them. Back when I first started with Boeing (1977), I worked in Renton and we'd go jogging at lunch time using a locker room/shower in a building on the Renton flightline. We'd jog by the 727s and 737s getting ready for delivery - and I'd noticed those big, ugly VGs on the 737 aft body, so I asked about them. The response I got is reflected my post - a few hertz vibration of the aft fuselage that made the cabin crew sick (the response was a bit more graphic, including if the frequency matched the natural frequency of the individual, they'd loose control of their bowels
). Now, it's possible that answer was total BS, but the source was normally pretty accurate.
The other part is a very good friend of mine was responsible for the APU installation on the 737NG - he got a patent and a cash reward for his idea for the "dual asshole" APU exhaust (look at the tail of a 737NG and you'll know what I'm talking about). He never mentioned anything regarding the VG installation affecting the APU. He retired about 10 years before me, but we've stayed in touch - if I don't forget I'll ask him about it next time I see him.