I always assumed they use some kind of tool to convert code into blocks. I refuse to believe somebody handbuilt anything bigger than a calculator in minecraft.
There are those that build entirely by hand; but the more common method is to use tools/mods like MCEdit to copy+paste whole sections of blocks. Then you can just build out one of each logic gate/larger section and copy+paste it all together into the full creation bit by bit.
In digital logic design, this is called a synthesis tool. In the design of real digital circuitry, you write a code-like hardware description using a language called an “HDL” (hardware description language) such as VHDL or SystemVerilog. Then a program called a synthesiser converts the HDL into a digital circuit.
Each module is designed this way then hooked up using busses and wires.
In real-life, you would then send the generated design to the manufacturing team