The issue lies not in late game fleets (which you are correct are basically invulnerable) but in early game contests where a properly tuned, fast player ship can take on huge fleets of frigates and destroyers (and even cruisers).
The problem is the combination of:
a) kiting and grinding the enemy down lets you win fights you otherwise would have no hope of winning without a fast kiting ship. If you can dart in with a wolf and get a single shot in on armor/hull before retreating yourself, you will win without trouble. This is a strategy that lets the player win impossible fights early, catapulting them into the mid and late game. This could be done either purely solo, or with a couple of similar speed tuned flanking buddies.
b) it is an incredibly tedious and boring strategy, once you have the piloting skill. (Its pretty exciting the first time you pull it off, but not the third.)
Yeah, it sounds like it was incredibly tedious and took a long time. It also sounds as though playing the game normally would have required only a somewhat larger time investment—except that the time spent would have been a whole lot more enjoyable, and thus (in my mind) a much better investment overall.
From my point of view, deliberately choosing to spend ten hours being bored and frustrated instead of spending fifteen hours having fun to reach the very same point (the midgame of Starsector, in this case) is incomprehensible. That puts me at a disadvantage in this conversation, and I truly wish that I could understand. That's not meant to be some lame insult; I just don't get it. I'm aware some people are that way, but it's beyond my understanding.
I mean, Starsector is a great game, right? How many other games like Starsector exist out there in this day and age? Why would anyone be in such a hurry to rush through as quickly as possible? Surely you're better off taking your time and enjoying it. It seems to me that many of you equate "best" with "shortest amount of time." Is this game a chore to you? Even if you just want to get to the midgame quickly, there are mods that will get you there in 0 hours. Modding really isn't worse than deliberately exploiting the game, and is much faster.
Trading boring real world time for the best strategy is imo poor gameplay.
That's true, and it's why I wouldn't do it even if it were still possible, nor would I consider it to be the best strategy.
A game's developer need not plug every potential exploit in order for me to recognize which mechanics can be exploited and avoid exploiting them. I consider games a sort of partnership between myself and the developer: They're building me a world, and I'm agreeing to have fun in their world. I have no wish to identify all the ways the game can be broken, and then break it. That isn't a condemnation of people who do like to identify and exploit weaknesses; it's their game, they can and should play it however they enjoy doing so (although, I don't always like being affected by design decisions that cater to them).
One interesting thing to note about the article Alex linked is that the earlier Civilization games (plus Alpha Centauri), despite not physically preventing players from exploiting certain mechanics if they choose to, are still considered the pinnacle of the series by the great majority of longtime fans. Alpha Centauri in particular is, in my opinion, the pinnacle of the entire 4X genre, and has never been surpassed. It's still installed on my computer, I play it single-player and PBEM (with a bunch of Brazilian guys, oddly enough) every year, and yes, it can easily be exploited by experts... but we don't.