I think the dark eldar are using the chameleon generators to look like a fleet they have encountered/destroyed prior to the battle. So, the enemy fleet is expecting an allied fleet (or some allied ships).
Otherwise, the most admirals could not be tricked by these generators - because the knowledge that it is somehow possible to mimic another ship is known to most factions i think (it's a piece of equipment every dark eldar vessel can use, and the mechanicus is experimenting with a similar technology too).
But thats my interpretation.
back to the rule-topic:
If your torpedoes (or nova cannon) are hitting an enemy ship, this would be an attack, wich leaves us with the situation: RAW, it is allowed to launch the torpedoes (and it is allowed to fire the nova cannon as long as you dont place the template on an enemy ship (you could target asteroids or something like that...)), but RAW your torpedoes can't attack/hit the enemy ship, while at the same time they have to attack their target because they have to by the rules.
So, the torpedo attack is not legal, the RAW way to solve thise would be:
yes, you can launch them, but you have to discard the marker without effect if it hits a ship (with active chameleon-rules), because there is no legal way for resolving this situation; the marker can't hit anything, it can't continue on its way, it can't stop, so its basically an illegal game piece at this moment.
But, if you define the launching of torpedoes as an attack (because it is a weapon system wich gets activated in the the same phase as every other weapon system), you could still launch them, but not if they would hit anything this turn or later if your oppotenent doesn't move his ships (you could fire the torpedoes between two ships).
This could be interpreted as "warning shot" fluffwise.
Another interpretation:
The torpedo rules are "core rules", while the faction specific rules are modifications to the core rules (for example: you don't have to question if dark eldar weapon battery uses core book rules or eldar weapon battery rules, they are a modification of the core book rules), so:
faction rules/modificated core rule > core rule.
This way, the rules of the chameleon generator have to be followed, even if core book rules are saying something else (this already happens; core rules say "its an enemy ship, you can do stuff with it", but faction rules say "ignore the core rules, you can't attack this ship while this rule is in effect"). So, you could also asume that you have to ignore torpedo rules if they would break chameleon generator rules.
Wich would lead us to: Torpedoes could be launched, but they would not roll to hit the ship because the chameleon rules prevent that part, and then they would continue their way (because the "comes in contact with another ship" part would never occur).
Conclusion: Just dont do it.
