Huge wall o text but most of this is going to be about description/nitpicky stuff as well as things that are almost certainly already on your todo list or will be inevitably noticed by you and fixed, but:
In the Mercy system, is the Abandoned Research Station supposed to way out off the edge of the map?
Tempest-S needs a ship system.
Fighter names are messed up (e.g. "Scale Support Fighter class Standard"). In ship_data.csv you should specify the name of the fighter wing in the name field, and the wing type as displayName in the .variant file. The convention for fighter wing naming is "[name from ship_data.csv] Class [displayName from relevant .variant]" when you target or mouseover them, and "[name from ship_data.csv] [displayName from .variant]" when you view in refit. You want something like "Scale" as the name in ship_data and "Support Fighter" in the displayName in the variant file.
The most important info in a ship description should be in the first paragraph because that's the tooltip, the rest all requires clickthrough to read the whole codex. For modifications of vanilla ships, that most important thing for me to know is how they differ from the vanilla ships. For example, the Shepherd Heavy/Light currently have the same tooltip description which gives absolutely no info about how they are different from a standard Shepherd and each other. You can fix this by just swapping those paragraphs around and rewriting them a little so the sentences still flow logically. This is done the clearer way round for the Hammerhead (TT), but the Lasher (Miner), Hammerhead (C), Cerberus (Miner) description uses a default-sounding first paragraph tooltip description and you have to click through to find out the important bits.
Heavy Borer Drones have a description for the fighters (which I can't find in the codex - it seems like fighters without a defined wing that are used by ship systems don't get a codex description?) but not the ship system.
Stuff I noticed that are missing descriptions:
Ship Systems:
Heavy Borer Drones
Rapid Repair
Phase Skimmer (Tempest-S Terminator Drone)
Weapons:
Desolator Cannon
Ships:
Scale
Mule Light
Mule Heavy
Lumen Scav X
Junk (has one, but assigned to "Junker" and not "Junk" in description.csv)
Scintilla
Tempest-S
Terminator drone for Tempest-S
Even something as short as the image descriptions for the ships in the OP would be pretty good in game as placeholder text until you can write a longer more flavourful description. Just a short note helps save a bit of mental bandwidth and get a handle on things when someone starts a new game and has a long list of unfamiliar weapons and ships to look at, even if the player can read the stats and test things in sim.
This is a matter of opinion, but consider changing names of (Scav) ships to (Salvaged). Then you can shorten the names from e.g. "Berserker (Scav) Custom Salvaged Freighter" to "Berserker (Salvaged) Custom Freighter" or "Berserker (Scavenged) Custom Freighter", which is shorter but conveys the same info.
There's also a bunch of typos of "scavanged" for "scavenged".
Also, the Heavy Frigate in "Shepherd (Heavy) class [Variant] Heavy Frigate" seems somewhat redundant.