Good questions. I don't necessarily have good answers, but let me give it a shot:
Q: Why is the Hyperion non-mil ?

A: Betelgeuse has a good answers--that's what I would say: The Hyperion is not under military control; perhaps it is so new that the Commonwealth doesn't have rules about it yet.
Q: Why is there armor that cannot be installed on a freigther ?

A: Battleships and carriers use heavier armor.
Q: You know of the bugs in present Point Juno ?

A: Need specifics, please. Which bugs?
Q: Why is a unidentified box confiscated ?

A: Ignorance is no excuse. If I try to take some unknown device through airport security and the device turns out to be a bomb, it will get confiscated (and I will be jailed) regardless of whether I know what it is or not.
Q: Why cant we power Gaian demo cannon ?

A: (1) Because the technology is available only to the Gaians. (2) Because not all superweapons should be available to the player.
Q: Is there a way to erase enhancement from shields, weapons, armor, ...?

A: Sort of. Adding a new enhancement (or disability) will erase the previous.
Q: Which ways are there to erase enhancements from shields, weapons, armors, ...?

A: I don't remember them off the top of my head, but I'm sure others know.
Q: Do molbidium and diamond field crystals the same ?

A: No, diamond field crystals stack (you can use multiple and they add up)
Q: Why must consumables vanish although they did have an effect ?

A: (1) ROM license agreement and DRM prevents multiple uses (to prevent piracy). (2) Otherwise, consumables would be too powerful.
Q: Why do Urak have no Encounters ?

A: They stick to their bases--they are not looking for trouble.
Q: Why do we always need to install an armor to repair it ?

A: To minimize another source of money.
Q: Why does savegames have to grow for about a megabyte each system ?

A: Each system takes about a megabyte to store.
Q: Why is there no damage shown for mines and missles ?

A: Missing code--should be fixed in some future version.
Q: Why does Dvalin continue to accept rares although he wont find any new developes ?

A: No good reason.
Q: Why has the stargate rod no image ?

A: Missing code/image--should be fixed in some future version.
Q: Why do I virtually die when I gate through the last gate ???

A: No more game content after the last gate. That's the end of the game.
Q: Why is there an autopilot ROM although every ship already has one ?

A: In a future version, there might be ways to wipe your computer, which would cause you to lose the autopilot.
Q: Why does everyone know that I'm on a journey to the core ?
A: 'Cause you tell them!
Q: Why do ships wreck
ing down face completely in another direction ?

A: Just to save memory--fewer images
Q: Why are the unknown chips, crystals and ammo boxes hidden in transc.xml but the unknown barrels are in the useful.xml ?

A: No good reason.
Q: Why does the freigther have tactial upgrade ROMs on start but not the fighter class ship wolfen ?

A: Freighter actually has a random ROM. The Wolfen is already pretty powerful. [Though arguable, the freighter should be weaker]
Q: Why do refugee-cargocrates have a loot screen although there can never be something inside them ?

A: Same screen is used for when the cargo crate has loot.
Q: How can a barricade fit into a cargo crate ?

A: Diagonally.
Q: Why do I always free all my slaves at the commonwealth ?

A: Because the Commonwealth won't let you do anything else.
Q: Why can't families inside the sung quarters free the other slaves after destruction ?

A: (1) They don't have a ship. (2) Otherwise, how will the player end up with the slaves (to either free or sell)?
Q: How can humans get into a sealed cargo container ?

A: They get in before it is sealed and seal it from the inside.
Q: Why are unid illegal items taken away but not unid military items ?

A: Not sure I get the question. I belive military items are confiscated.
Q: why is the Iocrym repeller an Energyweapon ? (no other plasma weapons are)

A: Because it generate plasma directly from a power source (not from an expendable cartridge). EnergyWeapons can be enhanced by Longzhu spheres.
Q: why the gaian Demolition cannon is an Energyweapon ? (it's thermo damage)

A: Same as above.
A: why the ion blaster is Specialty and the Heavy Ion blaster is ?

B: "Specialty" just means that it is not found in standard Commodity Exchange markets.