It really depends on your mod. In the stock game Heavy Photons deal double damage as Standard Photons, so you can utilize that as an upgraded torpedo as time advances. I really wouldn't increase the number of torpedoes on the same ship bc one would assume that if the ship remains the same (no added torpedo launchers/or phaser emplacements) only the payload would advance or the rate of fire. One thing to note is torpedo count isn't really accounted for in our game so I would only increase the amount of torpedoes per tube based on size. I normally follow this rule when making ship lists:
Frigates/Destroyers: 1x per Tube
Heavy Destroyers/Light Cruisers/Medium Cruisers/Heavy Cruisers/Battle Cruisers: 2x per Tube
Heavy Battle Cruisers/Dreadnoughts/Battleships: 3x per Tube
Battle Stations/Starbases: 4x Per Tube
Some others such as Carriers depends on size, if it's a Carrier in the DN range then 3x if it's a Carrier in the Cruiser range then 2x
Asteroid Bases and Base Stations also depends on size. But like I said, thats my take on it, everyone has different views on what their ship lists should be like.
As the eras advance I would upgrade the torpedo yield. Just like you upgrade the Ph1 to PhX on X-ships.