I actually did some more digging in regards to #3. I tried with unmodded game also so that I could isolate the issue. Result is that it just seems to be a bug which pirate player ships will only use the base hyperspeed for the component, regardless of tech (even with enough reactor power). This is is pretty limiting to pirates focused on smuggling specifically. Its really easy to recreate.
Just start a new game, game edit to give yourself the hyperdrive tech, make some freighters and speed up the game to watch all your ships fly (automated makes this easier). Upgrade your existing hyperdrive component tech with editor (so no retrofit is required). Immediately you will see all your state ships (even if already in hyper travel) increase to the new speed. All smuggler/non-state ships will stay at the base speed for the component.
A few things to note
- Newly created ships (built after researching upgraded tech) still travel at the slower base speed also, so this is not the issue.
- This only affects pirate games. Empire freighters work normally (correctly) when I did this same situation playing as an empire.
** This issue is definitely something to do with only pirate ships which appear 'gray/neutral' but are still owned by you. Actually ALL components do not receive upgraded effect (shields, hyperdrive, weapons, cargo). You can see this by upgrading your shields for instance as a pirate. All state ships (and even private mines, but NOT smugglers), will instantly get the upgraded shield strength. All smugglers will stay at original. Newly created gray/smuggler ships also have the lower shield strength. I believe the game must be putting these smugglers as an independent type faction which is just somehow aligned to you, but doesnt necessarily share your research (only looks at components in ship). This is pretty limiting to a smuggler-focused pirate. Most ships will travel extremely slow to try to complete a smuggling mission, often having the offered mission end before they even arrive.**
As a separate, but likely related issue. smuggler/gray ships will never retrofit. You can try to tell them to do so through the ship grid/screen (f11), but nothing will happen, even when they are not on a mission. They also never will upgrade/retrofit on their own (tried with leaving it on for a couple hours at 4x).
How do you go about submitting these type of bug reports? they are clearly unintended issues with the pirate faction.