Which races were you up against? I've noted this behavior from the Terrans, Drath, Altarians, and Korx.

Declaring war should cause them to build up a military, unless you're so much stronger that the AI decides to surrender. During my first TOA game when I originally saw this behavior, both the Altarians and the Korx developed into two of the strongest military ratings on the map (though the Korx were a paper tiger with pitifully outdated ships), but the Drath surrendered immediately to an ally.

I don't think this behavior is a bug, as it's a strategy some human players use as well. However, the AI shouldn't surrender just because its opponent is temporarily stronger.

Works the other way round too - declaring war too early will trick the AI into building hopelessly weak Fighters. Sometimes, when lacking any weapon-tech - they will be unarmed, or, in case of Iconians (or any race that traded for their stock armour tech) have 0att 1def which is of the same worthlessness.

Nope.  They were all quite happy researching up the weapons tree this time around.  Though it didn't do them any good, all my capital ships had defences as soon as I figured out what weapon type everyone was gunning for.

Just out of curiosity, I noticed at some point that there's nothing in the system preventing the creation of further 'exotic' weapons types in the tech tree - Has anyone ever done so?

I used the cheat mode to switch to the other races in a new game.  There's nothing obviously wrong (like the line of techs leading to weapons being completely missing) but they're choosing not to spend very much time on working towards getting weapons.

My theory is that the increase in time taken for weapons research in TotA, plus the slow tech speed, means that the AI considers Space Weapons a waste of time.  So unless you like going influence or tech wins, playing with a slow tech speed is completely unchallenging pointless and could be considered an exploit in Metaverse games.

So I've finally got them researching Space Weapons.

Unfortunately at the moment I don't know if that's a result of the tech tree amendment, or because I yoinked the aggression slider all the way to the right.  So I will have to start another game and see which it is.

I should note that I've never seen the Thalans fail to research Space Weapons. Assuming your theory is correct, this is probably because there isn't a special reason why they wouldn't value Computing techs.

Edit: Also, this seems like strong evidence that this is a bug. Given that the AIs do start researching weapons when attacked, and that a pacifist strategy is in keeping with their backstories, I considered it possible that this was just part of their Race Personalities. However, it now sounds like an actual bug.