How would you connect the wires? Up until now I have used jumper wires. Is that what you use when deploying a project? If my NodeMCU didn't have all the header pins pre-attached, then I would attach only the ones I need but unfortunately, they are already attached.
The answer is "stripboard".
I suggest learning how to use Eagle PCB CAD and design your own custom PCBs. Once you have the hang of the design process it's really easy to make boards for your project. Once the boards are designed, you can send the PCB gerber files to a PCB fab company for manufacturing.
Any reason you have to use the NodeMCU? Mabe the Wemos D1 Mini would have enough I/O pins to satisfy your project, and it comes without the header soldered.Speaking of de-soldering, I've been soldering since before lead paint was illegal, and I wouldn't try to remove the header pins from the NodeMCU.
Keep all/any jumper wires, or any wire that could be loose - away from the power rails and mains wiring !If a jumper comes loose and touches mains, a lot of nasty things can happen!