I encountered that (on cable disc brakes).

The first thing which I have found helps is to tighten the QR properly, which is to say, if you don't need to grab the fork for leverage it's not tight enough (once I read a Pinarello bike manual which suggests exactly that as a metric, it seems to help).

Second helpful thing seems to be to take some extra time to align the calipers and the disc as perfectly as possible and use organic pads. On my rear brake when it was time to replace the pads, I switched to organic and spent some twenty minutes aligning the caliper to perfection and the rear brake is basically silent now.

Front brake has semi-sintered pads which squeal during braking (on the upside... I don't need a bell because nothing shouts "get out of the way" as "SSCRREEEEEEEEECHHHH") and are prone to doing the "wump wump wump" sound you describe if I brake while not going straight (I presume this puts some sideways load).Going to get around fixing that, too, when the pads wear out (goes by quite fast, lots of uphills and downhills).