By RAW, linked weapons fire as one. Linked point weapons still fire as one. Thus, a linked pair of point weapons cannot shoot down two missiles in one round.
Only direct-fire weapons can be linked.
It's slightly unclear, but my suspicion is that penalties such as that from Broadside should not apply to tracking weapons beyond the initial shot. Countermeasures only last for one round, so there's no stacking that action, but the rules do indicate that using Improve Countermeasures will affect already-fired projectiles. In any event, it merely says to make an additional gunnery check for projectiles in transit without ascribing any action to it, so it's a free check.
Broad arc weapons can fire into other arcs, but are not mounted in those other arcs. By RAW, no.
On every round after the first, a tracking weapon's attack bonus resets to the attack bonus of the gunner that fired it. Any penalties such as Improved Countermeasures only apply for that round and then reset at the start of the next turn.
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The bonuses/penalties from Captain and Science Officer only apply in the round that they were added so no, a missile trying to re-target would not get those modifiers. A Captain could not aid/encourage/intimidate a missile that is trying to re-target.
As for a Lock On, I believe that bonus would apply if the Science Officer applied it in the round that the missile was trying to re-target. I also think Target System would apply as well.
The bonuses/penalties from Captain and Science Officer only apply in the round that they were added so no, a missile trying to re-target would not get those modifiers. A Captain could not aid/encourage/intimidate a missile that is trying to re-target.
As for a Lock On, I believe that bonus would apply if the Science Officer applied it in the round that the missile was trying to re-target. I also think Target System would apply as well.
Target systems is more of a debuff than a weapon boost.
I get what you are saying about science officer vs captain actions but that's just real world opinions, in game if the captain's orders aren't mind effects than they actually can intimidate missiles into being more missile-y. I can see it as an all apply or a none apply but not a selectively some boost missiles, others dont.
The captain isn't selectively boosting some missiles and not others. They are boosting the gunner who is firing the missile. And that actually does give a bonus... on the first round, when the missile is fired.
However, if the missile doesn't have enough speed to reach the target in that first round, then on subsequent turns the missile's attack rolls normalize. It doesn't get any bonuses or penalties that may be given to the ship's gunner that turn, because the gunner doesn't have remote control of the missile; it's independent. It recalculates range and any applicable penalties from its now current position to the target's now current position. A science officer on the target ship can still use Improved Countermeasures and that WILL affect the independent missile, along with any new missiles, because Improved Countermeasures is basically a buff to the defending ship rather than a debuff to the opposing gunner.
If there was a special type of missile (which I imagine we'll actually see in a book eventually) where the gunner does retain remote control, then yes, the captain could keep boosting that missile every round. However, the tradeoff for that would undoubtedly be the gunner using their turn to continue to control that one missile, instead of just firing more missiles. Since a missile is independent, the advantage is you can keep firing weapons in subsequent turns; that just comes with the price of losing direct control of the previously fired weapon.
Hopefully that helps it make more sense :)