1 Blockade will prevent everything coming out and in. Whatever happens inside the planet is the populations problem, if they get, erm, you know what i mean.
2- I think it should depend what kind of people you have, if its a military power and love wars, yes, they should love it to have that in the arsenal. I think how you get the tech is fine by me, once i recieved the super beam weapon that the ship uses, it was inside a planet or a base with the plans to build one equipment.
3- Depends, once the game have a better system of facilities, i think the devs should implement the Smart Weapons, meaning, like you say, less effect on other things, i have a game that uses this, bombs against populations and against facilities, and for that facilities should have Hull integrity. But bombs actually will have some effect in the ground, radiations, fires, explosions, holes in the ground, etc etc...
4- Set the tax at 0% , it will take time but you have to do it fast right after you invaded a planet or you will have that red face that once appeared to me because i forgot to set the taxes. Lucky up to now i haven't had any problems in rebelion.
*That* is the exploration that awaits you. Not mapping stars and studying nebulae, but charting the unknown possibilities of existence.