2. "Ship will become much more lethal after upgrade" random stuff from anomaly. What exactly that means?
This anomaly give the ship experience. Normal armed ships will level up when they win battles, giving them more hit points. This anomaly gives your survey vessel the same type of experience, but you need to upgrade it into an armed design to get any benefit from it.
4. Miniaturization bonuses - how exactly they work? I did try to compare stuff before and after, but most of the time they were of the same size...
Miniaturization increases the point capacity of your ships, while the modules remain (mostly) the same size. Many modules have their size scaled to the size of you hull, so extreme amounts of miniaturization can actually make the size of components go up.
To use numbers I know without looking, a tiny hull starts at size 16. The first level of miniaturization will give it 18, and the second will bump it to 24 - this is the minimum needed to put a construction, mining, or colony module on it, as all three of those modules are size 20.
5. Extreme colonization stuff. Heavy Gravity Colonization is all clear, I can colonize the worlds I couldn't before. But what's Advanced Heavy Gravity Colonization? My first guess was additional workable fields inside the relevant planets. Apparently not true.
As stated above, social/military production on these planets are set at 50% with the first tech, then increases to 100% (equal to a standard planet) after the second. FYI, the same works in reverse; if you steal or buy the advanced tech without the first one, the mechanics work the same.
and as a minor correction:
1. Planet quality bonus: increases the quality of each planet. Planet quality equals the total number of tiles of a planet on which you will be able to build after executing all the terraforming techniques (soil enhancement, habitable improvement, terraforming)
Not exactly. PQ is the number of currently usable tiles - terraformable ones are not counted. If you have a racial 10% PQ bonus and settle a class 19 planet, you will get only one bonus tile - the 10% bonus gives you 1.9 tiles, which is truncated to 1 rather than rounded up to 2. If terraformable tiles counted as PQ you would get 2 tiles.
Useless ones are 1bc found, morale and loyalty and soldiering ability increased by 1 %. Some others that I can't recall offhand
On small maps those are fairly insignificant. On larger maps, where you might get 30+ of each of them, they amount to something useful.