The roll could be kept opposed, and each side adds the appropriate DMs, but perhaps just one roll (by the players) is more simple. Then, the DMs could be potentially translated into something like:
If ship has military-grade sensors, +2
If any crewmember has navigation skill, +1
If any crewmember has electronics skill, +1
If any crewmember has naval experience (navy or scouts), +1
If any target is active (pinging, maneuvering), +1
If targets are X or more ships, +1
If targets are X or more small craft, +1
If target has "gone cold", -2
If target has stealth hull, -1 (per level?)
The value for success (detection) on the roll would be a fixed value, or one that also depends on distance to the target(s).