b) my Zenith bombard don't fire on anything immobile like force field and guard post? Why? And why it is not written in description?
It is, just not in the description of the bombard. If you look at the ammo type of the bombard, they fire "antimatter bombs".
AI forcefields (and a lot of other things) are immune to antimatter bombs. You can see that in the immunities list of the AI buildings. I assume it was done because otherwise higher mark bombard fleets could one shot almost anything from the other side of the planet.
d) why some of my ships like starships are in darker color when the rest is in bright blue? I did not put them in stand down. Same for AI ships, some are in darker colors?
The AI has ships in different colors because there's two AI players, and the default colors are red and darker red. If you change one of the colors in the new game lobby, you can make them stand out a bit more.
I don't know why you have multiple colors, unless you've got multiple players or you have zombie ships (taken with a botnet golem or insanity inducers). Zombies are a different color and you can't control them.
e) I'm not sure what it means (1)Wave(2)Reinforce when on AI planets.
As LaughingThesaurus said, that's the number of AI warp gates. Reinforce gates let the AI bring ships to defend the planet. Wave gets let the AI launch waves to attack you from that planet. If you take out all of the wave gates (the warp gate primarily), the AI can't launch waves from that planet. Doing this creates AIP, but sometimes you want the AI to launch waves at a specific planet and this lets you make it do that (kill the other ones near you except ones next to that planet(
f) How can I produce more of a resource (except by taking mines and crystals)? In previous version you could convert energy to a specific resource I think.
Take more territory. Alternately you can upgrade your harvesters using the science lab to produce more. Economic command stations also produce more than the other options, particularly if upgraded (I don't upgrade econ stations personally, I do upgrade harvesters).
g) My storage capacity is limited to 999.999 (yes, that's already quite a lot), is it possible to augment that?
Nope. But what you can do is when it gets that high, turn on a mercenary space dock and start building mercenary ships. Those are VERY expensive, but powerful ships. You don't want to waste any resources by sitting at the resource cap.
You can automate this if you select a mercenary space dock and push CTRL+0 to put it into group 0. Then go into the CTRLS menu (bttom right), and the control group specific tab set the resource limit for group 0 to 1800000. That'll have the mercenary dock only start building when you're near the cap, so it'll stop if you build anything else.