Unfortunately WAFU's aren't known for their knowledge of anything related to actual Ships...
The Navigation Bridge is generally positioned directly above the pivot point of the ship when under ahead propulsion. This is a useful feature when getting the thing into harbour (if you're going to navigate visually, which is often the case), which is occasionally desirable. Its nothing to do with Pepys, shouting or telescopes. Being high up is also quite nice too - you can see stuff. Which is why there are also windows. Being able to see stuff is quite good for avoiding other ships or big rocks and lighthouses.
Admittedly in carriers, the bridge is positioned by necessity in the island, which has to be displaced to one side. Moving it for'd or aft would completely bugger things up though... So its a bit of a compromise. I suppose parallel runways with the island in the centre would be the ideal solution. But then the FOD plod would really take forever, whilst being just as much a waste of everyone's time and effort.