Pretty sure the the smaller pitot type intakes have a spill door on the intake....this allows for subsonic flight.
With subsonic engines as you are talking about, look at the mechanism that creates the shockwave. When Mach increases, the spillage goes supersonic, creating oblique shockwaves around the exterior of the cowling.
Should a high bypass engine be designed to go to those Mach levels, the intake structure would be designed to be variable, so that as Mach increases, bypass flow is variable...maintaining correct pressures and flow.
As Owain stated, its all about maintaining the correct pressures.