This is definitely a common solution, but there are notable exceptions, such as Make Noise being only PCB mounted with the shaft not anchored to anythingā¦which is often a contributor to āwobblyā pot feel.
(not picking on MN or meaning to split hairs for @okyeron, hopefully just adding some perspective for @andrew/others)
I think PCBs are so common for DIY projects since otherwise youāre typically doing a lot of āpanel wiringā, often literally mounting the pots first and then hand wiring the whole thing. Trying to connect 32 pots on a protoboard actually sounds even harder to me, since you only have copper on one side vs a two layer PCB, which helps a lot in routing around the three closely placed pins on a typical pot. Wires, while messy, can at least move in three dimensions 
IMO, if you want a one-off and the goal is primarily to use the controller (as opposed to primarily a way to learn EAGLE or how to use multiplexers or whatever) Iād personally be inclined to:
- find the microcontroller dev board with the most analog inputs possible (Teensy 3.6 with 25 is the max I know of in a common dev board)
- lay out a controller that uses that many knobs
- get a bunch of āsolder lugā panel mount Alpha pots from Tayda - these should work
- wire all those pots as voltage dividers, each one going to an analog input on the dev board
- find/write/adapt code to translate those 0-3.3V ADC readings to MIDI or whatever!