Out of the three technologies listed, the only one which is easily seen to be relevant to the economics of planetary versus asteroid mining is the mass negation technology, and I don't know where you're getting that from.
There's a technology that references Mass Effect in ToA, and it describes mass reduction. There's only one mention of it I believe, and it's relatively obscure. I'll find it if I have time.
Hyperdrives in Galactic Civilizations appear to not work as well near large masses. Moreover, depending on just where the dead planets to be mined are, access to hyperdrives could at least as easily favor asteroid mining as planetary mining - after all, with something similar to present-day technology, Mars is a more valid mining target than any of the gas giants within this system, and is closer to Earth than the asteroid belt is. Both are close enough that with the apparent in-system hyperdrive speeds in Galactic Civilizations the travel time would be rather negligible, but mining the asteroids is still more economically feasible because it costs less to get the resources to a point where the hyperdrive is usable. Heck, it might even be feasible to strap hyperdrives onto asteroids and deliver them to the point of use that way rather than setting up any significant processing station out in the field. But that's more or less besides the point - the trip home has never been the major issue in making mining planets economically feasible when compared to mining asteroids, the major issue is getting the stuff off the planet in the first place.
Of course you're entirely correct. I recall a quote along the lines of "Once you're in space, you're half way there".
However, more distant targets require much more delta-V than nearer ones, even if you are traveling at FTL speeds or relativistically. This necessitates more energy expenditure and fuel, which in turn makes any theoretical ship design more reliant on large amounts of fuel/high-density energy sources. While this is an irrelevancy in game, this means that in real life it will frequently be vastly easier, faster and more economical to send vessels to nearby large gravity wells (like Mars and Venus). Provided the ships don't actually land on the planet (and mine with drones, for example), it would prove easier for them, energy-wise than visiting distant asteroids.
Obviously, asteroids, despite the above, have much richer compositions in terms of ease of access to valuable resources
Hyperdrives would tend to make this more extreme, as with a hyperdrive there's much less of an issue with the amount of time the return trip takes - if you're restricted to real-world physics, then the asteroid belt, being ~50% further away than Mars is, should take ~50% more time for the return trip, and since Mars is a several month trip one-way, that might be a sufficiently significant difference in travel time to worry about as far as the economics of the project go. With Galactic Civilizations hyperdrives in play, there is little practical difference as we're at most talking about a difference of a day or two, possibly even in the favor of the asteroid field.
Yes of course, but then again, the presence of artificial gravity and mass negation would make mining planets much easier as well, directly compensating for their chief drawback. Fusion, as I mentioned before, would also make energy requirements a non-issue.
As far as fusion power goes, fusion is not necessarily directly applicable to departing a planet's surface, as it will depend on how the reactors are set up, and whether or not a fusion-based thruster of whatever designs may be used in Galactic Civilizations are usable in close proximity to a planet's surface. Moreover, while access to fusion power may reduce the cost of providing the energy to move something from a planet's surface to orbit, assuming that it's an applicable power source, it will still take more energy to move mass A from a planet's surface to a waiting freighter in orbit than it would to move mass A from an asteroid's surface to a waiting freighter, even under the rather ridiculous assumption that the freighter waiting to take a shipment from an asteroid will wait at the same distance from the asteroid as it would wait at for a shipment from a planet. And unless the energy cost of whatever form of propulsion Galactic Civilizations uses is completely independent of the mass of whatever is being moved and of the gravitational attraction of whatever the departure point is, this issue will always be present even with magic 'mass negation technology' - especially if the power requirements of the 'mass negation technology' are proportional to the strength of the local gravitational field.
You're using quite a few assumptions about the technology the races of the fiction have available, I believe.
Ahh, I don't have time to expand on this further, talk more later?