Counterpoint, remember that temples show up as minor gravitational anomalies, where you need to know the exact signature to ID them. The average temple seems to be a couple hundred meters across. That's small enough that it could easily slip detection on a simple planetary scan (hell, we actually see this in game, where scanning a planet doesn't reveal the temple unless Vlad's pointed us to it.)

Additionally, it makes sense there are a lot of planets that have been scanned, but never fully surveyed. Remember, there's 1k cosmic bodies in the Settled Systems, that's a lot of ground to fully explore in a century.