You normally design hardware with a PCB. The pins just needs to reach through the PCB and hang out enough so you can solder them. The etched traces on the PCB will then take care of the actual distance between the components. This obviously under the assumption that the designer makes sure that high-frequency or fast rise/fall signal lines are short, i.e. that the PCB is designed so that components connected by fast signals are located close togheter on the PCB.

I get the feeling that you where planning on using a test deck where you just push components down in spring-loaded holes and then use wires to connect the components. That is normally a quite lousy way to build prototypes. The springs may not always make a good contact, and your wires may just look like they are pushed to the bottom of the holes. And the capacitance can affect your design. And the design can't supply higher currents. If you can't create a PCB, then use a PCB with pre-etched pads and solder wires between the components.