2000 points? Wow, you started out big! We 'only' did 1500 points and that was with 2 people on a side...and you did this SOLO? Kudos to you...
I'm not 'official' by any means but here you go:
1) It appears that Fighter Bays are valid 'Q' hits. The number of 'Q' hits on your damage chart goes up proportionally to the number of Fighter Bays, so it does appear that they are in the calculation normally.
2) Explosions....yeah, we had the same question. We played it with the explosions caused by Fighter attacks blocking LOS immediately. It did make for some confusion trying to remember which explosions were 'fresh'.
We thought that Fighters would be overly dominant too, but in practice, they really werent. Of course if you have no rapid fire weapon, few multi-bank weapons, and no Fighters of your own you are going to get hurt, but thats not much different than some of the other interactions in the game. For example, if you have nothing buy high factor shields and your opponent has no 'Ignore' or 'Half' Shield weapon (or at least multi-Pen weapons), its going to be rough going.
For my group, I've tried to keep most of the fleet designs in line with 'traditional' ship roles. So pretty much without even looking at the designs my players know that Frigates and Destroyers will most likely have some anti-Fighter weapons (with an occasional short-ranged ship killer) while the CAs and larger will tend to have the heavier ship-to-ship firepower. It keeps things consistant and allows players to focus more on fleet design rather than bogging down in the detail of each individual ship class. There are exception to the rule, but they easily identified (ie, a 'standard' Frigate should sport some AA weapons, but dont expect as much from a ship designated a Torpedo Frigate).
I've avoided Spinal Mounts so far. I had them in my test battle and didnt like the results of what basically boiled down to a lucky shot. In smaller (1500 and less) point battles a few successes with those things can make all the difference in who wins or loses. Thats just pinning too much on a few rolls for me. In fact, I've gone through and tried to make sure that most of my weapons are not incredibly dependent on one good roll that wipes out the target. More weapons or higher RoF is generally preferable to the One Big Gun that either smacks its target or does nothing. This is just purely a preference thing and I'm sure many people enjoy that thrill of the big hit or relief of a Spinal missing them, but for my group its just too much.
I agree 100% on the plotted movement. It definately sped the game up (we have a lot of analysis paralysis in our group...). It also makes for an interesting dynamic with regards to weapon ranges and arcs. It is possible to design some hideously effective short ranged weaponry, but the movement system prevents any form of guarantee that you can use said weapon. In most systems you can pretty much count on getting adjacent to the enemy, but in Starmada it takes some planning and a little luck. Once the range closes, the firing arcs really come into play.
Here's a quick question...do people tend to play 'open' or hidden? For example are players allowed to know what an opponent's ship does? Are ship records always considered common knowledge or do you just have to guess when a specific weapon or shield is KOed? We were playing fairly open (giving general information when asked...ie, "shields are about half strength, she's missing a few of the Spine Launchers and she cant make more than half speed"). Is there a consensus on this?