Yes your opponent will no doubt target engineer units with his arty, so if possible you need to have multiple engineering units in the hex you are trying to clear if it is in the LOS of your opponent. You might consider advancing non engineer units through the minefield accepting the losses it causes in order to create a LOS obstacle to the hex your engineers are clearing?
If an engineer is present in a mine hex it is considered to have cleared "lanes" through the minefield to allow units in column (travel mode) to pass through without the minefield "attacking" them. The lanes they create also causes a "penetrated" flag to be shown in the hex and this allows supply to be traced through the mine hex as well.