If my knowledge is correct, Shadow Maps are only usable, for static worlds. Should the lighting change then the Shadow Maps would look incredibly unnatural. I tried looking up some processes of how this was circumvented but no luck.
No, baked shadows/lighting (lightmaps) are mostly for static worlds, whereas standard shadow maps are dynamically calculated each frame and therefor useful for day/night cycles.
But for the life of me I couldn't figure out what I am supposed to do for the land or sky.
but there wouldn't be an actual choice between each tech is the most pressing to implement (I need better weapons vs I need better speed)
This could be mapped to ship classes too. You need other resources for building light fighter as for ion-cannon battle ships. The economy behind your empire will limit the choice of your fleet.
I want to capture ships instead of destroying them
This is an interesting feature which could be countered by customization.
combat is pretty much a stand-back and watch.
That's pretty cool, I like it. It reminds me of homeworld, when you watch a large battle evolving, your plans succeed or failed.
If you capture ships to research new technology (like Xcom), it would work. But if you capture ships to add them to your fleet, then customization could easily counter other game experiences. Customization gives the player lot of freedom, but lot of freedom reduces the desire for some interesting goal. It is the difference between "Wow, I want one of thos alien fighters, lets think about how to capture it" vs "Nah, it is easier to customize a ship similar to this alien fighter". Strategy lives on limited options, because the decision you need to make have more impact. Therefor customization could counter some other strategy related features.
That being said, I'm a bit scared of lacking depth.
This is an effect of knowning our games to the last detail. As game designer we are bad game testers. A strategy game have lot of knowledge based challenges (no skill challenges), therefor you are more or less already a master of your game. An other player will have an absolutly other game perception. If you would make your game challenging for yourself, it would be impossible for others So, less is often more.
16bit for saving the depth is quite low (I dont mean the z-buffer!). Best to test the depth buffer first. Just output the z-value and compare the images. Do you see machband-effect or other artifacts when using a low fov value.