If starfighters have a pierceable canopy rather than the cockpit being located in the midst of the ship in exactly the same manner as you described, I would not expect a different design philosophy applied to the larger vessels. Indeed, what we have seen from the rather sizeable
Anaconda and the capital ship battle video suggests that windows remain an important feature for larger vessels as well. For what it's worth, aside from being a rather classic aspect of science-fiction, windowed bridges also have the advantage of specifically
not relying on cameras that would effectively blind the commander to what's going on if this system's power is disrupted or the lenses themselves are damaged in battle.
However, I would welcome additional emergency systems such as bulky armor plates that you can manually lower down in case a window is pierced, to prevent atmosphere from leaking out at the cost of visibility, forcing you to pilot the craft by sensors (and perhaps an extended holo?). It would be neat if the player could also "jump" into the seats of any turrets the vessel has installed.
Technically, large vessels should perhaps not be piloted manually at all, but rather just by plotting a course and have the computer do the rest (representing your crew executing your orders), but this would probably be too boring?