I'm with you on Bridge Windows, unnecessary, especially when you want to Bury the Bridge like I do =D.
But following your logic of the Bridge being protected like a giant groin guard, wouldn't MORE Super Material Groin Guards in terms of floors with the same level of armor in between add more protection on all sides?
Imagine all the Structural Trusses / Floor Plating / Walls made of similar materials, like the hull?
Just look at how much damage the Defiant took on it's hull with Ablative armor, now stack that by all the extra deck layers you can have in between the outter hull and the Bridge Room?
That's just MORE layers of protection if you design it right.
Engineering is always a trade-off. Super dense materials are good protection - but they also make your carry around a lot of heavy stuff, this make you slower and less flexible.
Basically, if you wear a groin guard, you can compete in a lot of challenges. If you wear a full-body protection, you can only compete in a very specific combat scenario.
On a spaceship, it would make sense to give only the most important parts the most protection.