I figured it was possible to run out of points, so I've tried to avoid charting paths to distant systems as much as possible and only going along the routes I've discovered, trying to keep my warp points around 20, just in case. Good to know though! I'm running out of Extractiums at this point too so I'm going to Kiava to unfuck that situation, I imagine that's the planet that I'll be able to get more of those from. Though, given that derelict mechanicus ship from Kiava that I came across, I might be wrong.
On my first attempt at the game I ran out of nav points and caused myself considerable frustration trying to nickle and dime new ones from events. On my second attempt at the game (I played part way on Daring to get a feel for it then started again on Unfair with the DLC for my real play), I was so conservative and willing to eat ship events that I ended up with a surplus and had enough to make some really long routes between systems - this proved useful when I need to rush somewhere to deal with a crisis. Frequent references to me getting to Dargonus in time to save people feel good, man.
Extractiums are even more precious than navigator points. I used them unwisely and then ended up farming small encounters trying to eke my rep up with the Explorators in order to acquire some more so that I could mine some desperately needed Adamantium. Was a real block for a while because I didn't want to go down a non-preferred planetary project route but I couldn't do the one I wanted without the Adamantium.
I've honestly come to like how Owlcat is willing to let you completely fuck yourself over. I even enjoy the way respecs eat into your profit factor. Makes poor judgement consequential.
I have not, good to know that exists as well, I assume it acts as an escort of sorts? What happens if it blows up? Do you get a new one or is that it? I think the two colonies I currently have are both working on their third projects, don't remember seeing anything in regards to building/being rewarded a ship.
It exists as a rather weak escort. It has none of the upgrades you add to your own ship over time and is not directly controlled. However, it is willing to die for me repeatedly soaking up enemy cannon so it's alright by me. And yes, it comes back.
I don't recall the project names that get it you though they're clearly marked. If you look through your projects you should see them. IIRC, one is Navy related and one is pirate related. Fairly certain it's not possible to get both.
I'm going to be blunt - if you're finding the ship combat unbeatable, you're just not good enough. Sorry, mate! You either need to try out different tactics or more carefully build up your level and equipment or both. Some of the battles are very difficult but they're all beatable. Sometimes it just takes planning and changes of tactics. You should definitely be seeking out the escort ship as a priority unless you're playing on Normal or something. One of the fun aspects of this game is that it's possible to screw up before you even realise you have. You need to claw out every possible advantage you can and that's what I like about the game. I can get aeldari torpedoes? But I'm dogmatic and that's a little heretical... which do I choose? Fuck it - I need the torpedoes to take on the _________. Can't serve the Emperor when I'm dead. A little heresy wont harm, right? Right?
Space combat is pretty good overall, just got some niggling issues that irk me personally. Most notably, shields. I have to take down an enemy's shield in order to do damage to them, but even the scrubbiest of pirates could just politely ask my void shield to go fuck itself and it would, causing me to spend a ton of scrap on repairs that I'd much rather not have. Less of an issue now that I have a slightly stronger shield generator, but it feels like a case of Owlcat going "How do we make space combat challenging? No ideas? Alright just make the shield only work sometimes, that'll teach 'em."
Try better guessing which shields to reinforce, better generators and armour and better manoeuvring to not get pinged on the same side so often. Difficult with eldar I admit, but there's always room for improvement. Honestly, armour vs. damage is kind of a staple of RPG levelling. I don't do enough damage to hurt them / I can't soak enough damage to survive them... these are things that always scale with advancement and differentiate tough opponents from weak.
I ran into several encounters early that I barely scraped by or even lost on first attempt, but with a couple of upgraded parts I can cruise by most encounters relatively easily. Took out 5-6 Chaos ships outside of Kiava without sustaining a single point of damage, for example.
There you go - maybe you're just expecting more guard rails about what you encounter. The games not really like that. You can pick and choose when to approach many of the encounters. If you're not ready for it yet, do something else. Clearly you're improving.