So, I have a the Kestrel kitted out to the teeth with lasers and 3 shield laywers, as well as a anti ship drone and a missile defense drone. Get to the endboss for the billionth time....
And I then realize I have exactly 0 missiles. Sad times all around.
The repair stations give missiles, and don't disappear after using them once, so if they are placed somewhere not terrible you can get +10 missiles before the fight.
Also:
The Zoltan ship is lovely. First off it starts with three zoltans, which will end up saving ~100 scraps in energy costs (or let you use even more equipment then you can with a normal ship), not to mention they are super good in ion storms and can semi-ignore ion effects.
Secondly, its super sheild is super great, it functionally lets you ignore the first few missiles and usually the first two bursts of attacks, saving you on average 3 health per battle (if they have at least 1 missile and you don't have a defense drone, if they have a beam drone its near useless however). It also lasts long enough so you can pre-vent rooms to screw up boarders when they tele there, and even starts with doors two.
Finally the haldbers beam is great. It can *always* damage 4 rooms (although there are times when damaging 3 system rooms is more important), and on a few can damage 5 rooms (8-10 damage). Yeah, the missile launcher kind of sucks, and you are screwed VS a enemy with 2.5+ sheilds, but if you never find a weapon you are screwed no matter what ship you use.
I do agree that the zoltans limited health is a pain, but you can't get 1 shotted by anything. A bit of bad luck combined with not healing can take you out (eg. a breach missile hitting you while your health is low cause of a fire), but if you keep their health up they are fine. Boarders aren't much trouble due to the supershiled+starting with doors two.