I just failed 'Clouds of Vondoru'...

You can take out superstructures of fortresses and cartel stations in a single hit, completing a hidden bonus mission to gain more credits/coms

I can't get the 4th one to fire

Its not bugged. You do have 4 protons. You have one in your tube already. 3 means you have 3 reloads not that you have only 3 missiles.

An interesting take on it. However, when I first installed my launcher it indicated 4 and did so until I failed one mission (having fired one torpedo off) for the first time and from then I only had 3 available, no 4th. Uninstalled and sold. Picked up a new launcher later on yet it only registers 3 but has 4. I believe it is a bug. That being said, missions are far easier without Protons except for "Kahless Expanse" where they are not required, yet it is one I have recurring problems surviving. The others are beyond easy, just trickier with Protons.

There are 4, the one that is ready is the 4th one.

You can. Tap for regular missiles, hold for Protons.

Necro troll strikes again!!!

Not in some Space Missions. Once the targetting comes up for a torpedo ( as it does in "Zosha Advance") you cannot fire missiles no matter how many times you tap the mouse button. If this one gives you trouble, removing the launcher is the only option as only then do missiles alone become n option (generally 4-5 per generator).

If only that were true. My ship will destroy all the cannons BEHIND the shield generator, but refuse to fire on the shield generator if I have the torpedo tube installed. Seems to be specific to the Cruiser, as I can fire missiles at corvette shield generators.

You can fire normal missiles at the shield generators in the seconds between launching a proton torpedo and it hitting its target. That's how you take out all four shield generators AND the main bridge for the daily bonus. Might take a couple of tries to get it right, but once you learn the trick it's pretty easy to repeat.