To add on, real fighter aircraft frequently have smaller inlets than EDFs need. If you make your inlets smaller and need to add a cheater inlet, you're adding drag. If you just want smaller inlets for looks though, a cheater hole is a good option.
To add on to quorneng's answer, you want inlets 95% to 110% FSA and a thrust tube outlet 95% to 85% FSA. Even with a thrust tube and inlets the same size the fan still produces thrust (you can tell inlet and outlets speeds are the same in this case from continuity) but that is because the fan accelerates the air external to the ductwork and it is a less efficient setup. This even goes for a larger thrust tube than inlets, but efficiency losses continue to get larger.