That would actually make them easier to spot, as they'd need to flip around for a breaking burn roughly equal to their acceleration burn, pointing their engines straight at us. (Assuming they want to stop by and say hi, of course. If not, then there's not much to worry about.)
If they intend to go straight through Earth at relativistic speeds (to establish a hyperspace bypass, perhaps?), then there's really not much we can do about it anyway. :p
Fusion drives wouldn't allow these ships to get anywhere near the speed of light, so we would have ample time to see the light they emit long before they arrive.