The text issues are well known --- I myself submitted a ticket on it and I was informed they are working on it with no ETA.   Sometimes they are just annoying but other times I can't figure things I need to understand.   Hopefully the January patch will  help with this.

In my experience enemy starbases and shipyards remain there and unusable, as you say.  If I have defeated the last colony of the empire, then remaining ships become pirates.    I have to DoW on the pirates to eliminate any of this stuff.   I have also noticed at least once that an Empire I had totally defeated continued to ask me for peace in the diplomatic channel.    So I agreed, I figured if they are dead, let them rest in peace.    I feel confident that the results of combat will be much improved in the next beta patch, where hopefully we will also see the combat viewer.

I might mention that although tactical decision making will not be featured, I think seeing what happens in the viewer may be critical for understanding why you are winning/losing.

Having the fleet size register in a bubble without clicking sounds very good, I tend to have to do a lot of clicking.   But I have an alternative...couldn't this be included in the planet list on the right?   Might have advantages/disadvantages, but it sound like the programming required might be a lot less (just guessing).

Most of the time when I have killed off an empire (last colony taken over) there are a few enemy ships left, and they do not disappear, they become pirates.    At least that is what I conclude, as when I attack them I get a message that I have to declare war on the pirates to attack them.   Kind of a weird mechanic as I was just fighting the same ships, and then because their empire fails, I have to declare war again to attack them.  I have killed pirates several times, however, I don't know if, for example, they will attack me at any point if I let them go.

 I expect that pirates will be much more fully fleshed out as we go along (or possibly, if they can't be worked in, dropped completely - don't what that!)    Pirates could possibly prove useful in some ways if they spawned spontaneously from the start of the game.  (Of course there should be a way of managing how often in the options, just like barbarians in Civ).    First, they would provide a reason for guarding trade routes.   Not sure how that would work though.   Secondly, they might be a brake on reckless colony expansion, e.g., unguarded colony ships would be highly vulnerable.   And they would provide a reason for early garrisons of planets, shipyards, and starbases.

That sounds like a bug about rushed production.

Er, I think you might be posting to the wrong thread?