In general, normal wear can cause the rotors to become groved. The pads wear "into" the rotor during regular use. At some point, the rotors may need to be turned or replaced, and the pads may need to be replaced. Both the turning/replacing of the rotors and the replacment of the brake pads is done at the same time. Few if any professionals will attempt to "short cut" a brake job by just doing one thing.
depends on the condition od the pads. If worn or have groves etc from the rotors then replace.
friction
Hot spots are caused by over heating the rotors Causes: "riding" the brakes, faulty brake components, general abuse
Bad rotors
Excessive or heavy and continuous braking may warp brake rotors. Braking hard (heating the rotors a lot) and then going through water (which quickly cools the hot rotors) may also cause the rotors to warp. If the brake pads or brake rotors are getting thin, the rotors will warp more easily.
Brake rotor/rotors are out of round / warped. Check rotors and REPLACE as needed.
bad brake rotors or alignment shocks struts
I don't know if you are saying you have the new hubs and rotors and still have pulsation, or if you are asking what causes pulsation. If you have pulsation on slowing this is due to warped rotors, and you need to change the rotors and the brake pads, not the hubs. Not too expensive: 2 rotors and brake pads for my Pontiac is about 55 bucks. DIY of course.
Front rotors could be warped. Replace
Do you have anti lock brakes that might be it if not your rotors maybe warped
worn pads change your brake pads and get your rotors machined while your at it
Brake calipers are the hydraulic devices that wrap around the rotors and pinch the brake pads into the rotors when you stop.