A few thoughts:
Re: Protective suits for engineering crew on Starfleet ships: They have them in the Kirk-era movies. I don’t recall seeing them any other time.
Wasted volume in a spherical ship: Sure, most human equipment is designed for square-angled rooms, but a ship would need to carry plenty of non-solid essentials like water, air, and fuel, all of which could be stored in tanks along the hull, and which could be whatever shape is needed to suit the interior of the ship.
Armor vs. shields: In the Honor Harrington books, the emphasis is on shields due to the type of weapons being used (and the availability of powerful defensive fields formed by gravity manipulation technology). Bigger ships still carry plenty of armor because they’re big enough to carry enough armor to still be useful after the shields take most of the sting off. The justification seems to be that once a ship gets that big, stripping the armor off doesn’t make enough of a difference performance-wise since the limiting factor is inertial dampening rather than available thrust.
One of the anthology collections included an in-universe article about starship design that stated that warships in the Honorverse often carry their hydrogen fuel tanks (lots of hydrogen being needed for their fusion reactors) outside the crewed portion of the ships, with the fuel itself being set up as a sacrificial layer of protection. The tanks are basically designed to blow outwards (like the magazines in a modern tank), effectively giving the ship a layer of ablative armor.
That said, I hadn’t read of a single ship in the Honorverse being saved by its fuel tanks, but I guess it’s a “Every little bit helps” design philosophy.
For Babylon 5, only some of the human ships use rotation for gravity (the Explorer ships, B5’s version of the Starship Enterprise, basically, and the Omega Destroyers, their equivilant of a Battlestar). Most of their ships have the crew strap themselves down all the time (Hyperion cruisers, Nova dreadnoughts), and some of their newest ships have the newfangled artificial gravity (the Warlock and Victory destroyers, with the latter finally ditching the humans’ blocky geometry design style).
While the human Starfury fighters have the pilot lying down (or, from the viewer’s perspective, “standing up”), the Minbari Nial fighters with their artificial gravity instead have the pilot lying down to give the ship the smallest profile possible.