In the Star Trek: Next Generation Technical Manual, it is mentioned that the Bridge module is replaceable. This makes a case for why the bridge should be where it is.
The concept of the replaceable bridge module originated during Star Trek V, when we were working with Herman Zimmerman on a new Enterprise bridge that was quite a bit different from the one seen in Star Trek IV. We rationalized that this was because the bridge, located at the top of the saucer, was a plug-in module designed for easy replacement. This would permit the ship's control systems to be upgraded, thereby extending the useful lifetime of a starship, and would make it easier to customize a particular ship for a specific type of mission. This concept also fits the fact that we've seen the main bridges of at least four different Miranda class starships, the Reliant (Star Trek II), the Saratoga (Star Trek IV), the Lantree (Unnatural Selection) and the Brattain (Night Terrors), each of which had a different bridge module.
The problems with this placement are clear, but we also see that unshielded starships are extremely vulnerable. If an enemy wanted to destroy your ship, they would be better served by targeting the reactor. If they wanted to kill the bridge crew specifically, they could always beam them out into space, no matter where the bridge was located.
