Scout starships become an excellent way to do the scouting, in those games. I can't recall, but mark IV scouts may also be able to bypass them. You can also send strike forces to just kill the counter-spy unit specifically, if there is only one or two of them, but if you are playing against a counter-spy type AI then they will be all over the place and you'll have a really hard time scouting in general, and will mainly need to rely on scout starships and careful positioning on the map to make it so that your scout starships have lower distances to travel (and thus can survive).
