User blog comment:The Milkman/Extended Expectations, Part II/@comment-1441235-20120629062602/@comment-1221773-20120629071907

As sentient starships, the Reapers may depend on other methods to analyze their surroundings than detecting the visual spectrum. There's not much you need to see when traveling through space, it's mostly empty and objects are vast distances apart. Navigating by sight is impractical; think of a submarine, when they're under water they rely on sonar. If the Reapers are designed to interpret any object emitting an IFF signal as friendly with whatever scanners they have and they lack the means for visual verification, then the Normandy could get right next to them.

Similarly, recall Legion's loyalty mission on the Heretic Station in ME2, the station lacks windows because they're viewed as a structural weakness by the efficiency-minded geth. This allows the Normandy to dock with the station undetected with stealth systems active, even though if the geth added cameras to the station or kept windows they would see the Normandy plain as day.