Jacob hid a message inside Gaalsien's database, containing a video addressing Rachel. After all these years he still believed Rachel would come along.
The Gaalsien Flagship in the final mission just won't budge, even if you shoot it with the Taiidan orbital laser. Considering where the technology came from, it could be that the Gaalsien use spaceship-grade armor meant for war they've gotten from the wrecks around Kharak to build the Flagship.
The Kharaki know how to build cities, surviving harsh conditions but don't know anything about a rain cycle. After all, they're from a different planet.
Calling an army a fleet? Maybe the term just stuck with them.
The term is All There in the Manual; their early desert craft were wind-powered, and they still consider desert warfare the same way we consider ocean-going war. The armies they use in the temperate regions are more conventional.
Why aren't the ships and Kill Sat mentioned in the original Homeworld? Because the tech is so similar to their own that the logical conclusion is that the ships actually belonged to their own race, and thus probably got stuck on Kharak for the same unknown reason as the Hiigarans. Which also leads to...
The reason that the Mothership was made to survive any situation is exactly because of all the crashed ships: all of them were heavily armed and armored, but showed no signs of battle damage. Thus, the reasonable conclusion is that space is clearly dangerous enough to warrant military grade protection, but anomalies would actually be the bigger threat.
The crashed ships also explain why the Mothership crew managed to make new ship designs so quickly: they could already infer the basics of space combat from the crashed ships, so all the researchers actually had to do was adapt existing designs to the most recent tech.
The discovery of a Taiidani Kill Sat orbiting Kharak and crashed Taiidan destroyer in the desert explains how the Empire found out about the Kushan's hyperspace test so quickly; they were monitoring Kharak for at least a century before the launch of the Mothership in HW1, maybe longer. Maybe A LOT longer...
Add a bit of Fridge Horror; it's possible the Taiidan were aware of the Mothership construction in HW1, and let it proceed so they'd have an excuse to wipe out the Hiigaran exiles once and for all.
If the devs planned it from the start, Kharaki probably reacted really bad to the betrayal of Sakala's crew, to the point that they nearly erased Siidim from pre-mission records (the document that came with the game) in Homeworld 1.