I am using an Arduino to read/control 3 DC motors with encoders (using the Adafruit motorshield featherwing and a 12V supply), 6 limit switches (2 per motor), 2 sensors (current and lux), 1 push button, and 1 relay (for the 12V supply).
I've got everything soldered on a perfboard using dupont connectors and standard male headers to connect the motors/sensors/encoders/switches. I would like really like to clean up some of the wires and put together a custom PCB. Could I have some suggestions for wire management? Dupont works ok, but it does feel little "wobbly". I considered something like this PCB from OpenSprinkler, but I think it the enclosure would get really big considering it's 3 wires to encoders and 2 for limit switches.
I assume you are referring to the screw terminals used on that module. As you say, they are bulky and better suited to jobs requiring large currents.
To move one step up from duponts on headers, consider JST type or JVT connectors. These solder into the board like headers, but have a plastic head shell that engages on each side to provide some mechanical support. These can be bought from the usual ebay/banggood/amazon in boxes of 200 connectors of various pin counts.
Using the proper crimper is highly desirable, but I have had success (1) using the wrong crimper, carefully, and (2) crimping lightly with needle nose pliers and then soldering the connection.