I think it looks better to have the name plates in use wherever possible.
In fred2_open, go to ship editor. Select the ship you want. Right at the bottom of the first column is a button labeled "Texture Replacement".
It bring up a "Ship Texture Replace" box with drop downs. This is the list of textures used by default for that ship.
In the Severed Dreams mission for example, go to the Omega class Alexander. The "Old texture" is eam_omega_01, the default blank one. Replace it with eam_omega_alexander. Do the same for the glow map. Paste eam_omega_alexander-glow on it's line.
The Nova's also have shine maps so that would need to be replaced for them as well. The list of name plates are all located in the maps folder. There's a bunch. When you save the mission it will update in Fred and you'll see the new name plate.