First off, realize that the Italian torpedo boats were not designed to take a number of hits and survive. (In fact most DD and smaller ships rarely survived 3-5 six inch gun hits unless they were all to superstructure areas).
For example:
link
Note the last paragraphs of this wiki. Even at night, and close range the TB's didn't hit very often for their high rate of fire due to the lack of night fire training and national doctrine.
That being said, I have found that a number of rules overstate the ability of gunfire to hit, especially at their long or extreme range. When you consider that US BB gunfire practices of the 1930's considered 3% hits to be an excellent result at over 25,000 yds (25 Kyds) could you expect light guns on relatively unstable platforms to hit often at their long/extreme ranges?
In my opinion, many rule sets allow for higher to hit percentages in order to keep the game interesting. After all, few players want to roll dice turn after turn with rarely a hit occurring. Rules may do this different ways, the most common I think, is to say each round of gunfire is 5+ minutes worth. So when you get a result of 1-3 hits on that turn, you gotta remind yourself that those guns have fired maybe 100-300 rounds that turn.
Anyways, back to your original question, how to handle light ships. Keep them at longer ranges, if they are tasked to protect ships, use smoke and evasive maneuvering. Their main threat is not their gunfire, but their torpedoes. If you read the wiki link above, you will note that it was a night engagement, when light ships will have the best chance of closing to effective fire and torpedo range. Even so, the light cruiser got 4 hits on the TB effectively sinking it. Note that the CL took only few hits in return.
I'm not sure how NT handles targeting. Many rules will adjust hit possibility by the ship size. For example, gunfire final results at TB's might be adjusted by 1/2. They usually pick a ship size of say 600 x 50 ft and that area size is considered 100% for gunfire.
Evasive maneuvering also is some adjustment to the final to hit number. Type of gunfire control also plays a part in the to hit number: radar enhanced, modern directors and plotting, stereoscopic rangefinders only or just local control play a part in the ability to put the gun on target.
In your last game example, I would've employed a CL with the 4 spicas as a screen between the Zara and its close escort, using smoke, salvo chasing, and staying on the unengaged side of the smoke to keep the french from advancing too quickly. The threat of getting torpedoed upon closing the smoke screen would be enough to keep the French from acting rashly by closing the range. As Italian Cmdr, I would be loathe to send my 4 TB's against any 1 of the French (super)DD's, let alone 3 of them, knowing how few hits they can absorb and still be effective.
TB's as you appear to be learning are a fragile asset. Better than nothing, but not by much.