Good of you to remember that "sensor bay" concept from the TNG Tech Manual...
Well that, but I'm also inspired by someone mentioning this as an explanation for the room where Picard showed Lilly the Earth in "First Contact." Seeing how it was only accessible from the jeffries tubes, there's no reason for that room -- or the exterior door, for that matter -- unless something like a sensor probe or scientific instrument was supposed to be installed in that bay and deployed into space when needed.
In this case, the "sensor bays" are installed behind (most of) the visible windows on the Enterprise. Most of the auxiliary sensor modules are the size of pickup trucks and so they fill basically the entire bay. Of course a few of those windows are just windows