Fleet module bonuses don't stack with the same fleet module bonus.  So you only need one ship with a particular fleet bonus per fleet.  Unless you want some redundancy in case the first ship with a fleet bonus gets destroyed.

Concerning your alliances question, when the first enemy attacked you, were they already at war with your allies?  If so then, of course, your allies will not declare war again.  I've personally never seen an ally fail to join the war when I am attacked.  (Though they do not join the war if I am the attacker.)

IIRC, you *must* ask for help by suggesting an attack by an ally against your enemy (be it common or otherwise)... it's a deal that they have a right to refuse or not. There are other gameplay situations that trigger reactions (such as shared ethics) when YOU attack one of their allies.

In summary, the AI algorithm decision process is in no obligation to honor their alliance **UNLESS** you provide an incentive (which is represented at times by SuperOrganizer ability, btw).

In diplomatic terms (real & rational), an alliance doesn't imply someone is going to fight your wars.

Has it ever occured to you that maybe, THEY have no contact with that race but you do?

Diplomacy implies reputation(s) to exploit or waste. If you're a war monger allied with someone who doesn't want troubles with THAT new enemy, they'd be surprised enough to brake their alliance with you if only to protect their empire.

To clarify how Atlas modules work:

-Each Atlas module can provide bonuses to 1 or more bonus types. Only 1 bonus for each fleet type bonus, can be in effect at any given time. Only the strongest of each type takes effect, while everything else (including other bonuses of equal power) takes the redundency role in the event you lose ships.
-Each ship may only carry 1 Atlas module.
-There is a Fleet Warp Bubble bonus type, but it isn't considered to be an Atlas module so you can install a Warp Bubble on a ship already carrying an Atlas module.
-Not all Atlas bonus types affect the whole fleet. There are 2 personal types (attack and defense, anywhere on the map, no fleet wide bonuses). There are 2 ZOC types (attack and defense, like personal but only in your area of influence). There are 2 fleet wide bonus (attack and defense, affects the whole fleet anywhere on the map). There is also 1 first strike bonus type (attack bonus, like fleet wide attack but only works for the first round of combat and only if you start the fight).
-All Atlas bonus types (assuming no redundency) stack. As such, using a bunch of ZOC attack ships with a fleet wide attack ship can significantly increase the attack power of your whole fleet, atleast in comparison to using only 1 or the other.

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Sigh, I need to update my TA 101 guide...

Glad it was of help. I've spent many, many hours over many games trying to figure them out.

If they weren't on that list, then your ally must have had some treaty with them.  Or were already at war.  Those, I believe, are the only reasons to not see a race on the 'attack' list.