I have had odd noises over the years which wound up being:
Dry polymer suspension. Take it apart and grease the bolt. Mine squeaks more with pedal stroke than bumpy road.
Seat post isn't quite tight enough. This may involve replacing the sleeve and I wound up paying an LBS to do this. As I had overtightened the QR before, I had ovalized the post and had to replace that too.
The SA 3 speed made odd noises, especially in high gear. I resolved that by putting synthetic 5-20 motor oil in the hub through the shifter opening in the axle. When it gets a little noisy I put in another cc or two. The downside to this is the hub slowly leaks out the oil, so I switch to a 1 speed wheel if I take it in the car to another city. The upside is when adjusted properly it shifts easily and runs much more quietly.
I have replaced the ISO bottom bracket with a JIS Shimano and there have been no bottom bracket noises after that. BTW no issues noticed with an ISO crank and a JIS bottom bracket.