You using the GWX mod?
At first I had the same issues. I'd fire a tube, check the torpedo map, and it was headed toward Antartica or somewhere I didn't point it.
I've found the best way to work is be methodical. Always line up your bow perpendicular to the ship's path. Never try to "wing" torpedo shots at higher than 700m, they're just too unreliable and the AI is just good enough to move the 4 degrees it takes to miss them entirely. You have to stalk every ship and set yourself up for the perfect shot, every time. Otherwise you waste ammo, end up having to surface and use the deck gun to kill freighters. Which becomes virtually impossible later on in the war. If you're using the GWX mod, this is actually the majority of game play, trying to make distance on ships that move faster than you while you're submerged, managing the distance to the ship so you can surface to flank it at maximum speed, managing your CO2 levels and battery power on top of all that. And that's before anyone with an interest in firing BACK at you really comes into play.
Sometimes just plotting a good intercept course when you spot an enemy contact can put you in a good position to get an easy kill, rather than charging straight at a ship at flanking speed to close the distance as quickly as possible. The training missions give you an....incomplete sense of what it's like trying to chase ships down in the open ocean.
I don't rely on the firing telemetry data because it's always behind on where you should be shooting. Still, it gives you a general idea where you need to line up your shot. Basically, at 700m, firing at the leading edge of the ship (when your boat is at a 90 degree perpendicular angle) will almost always guarantee a direct hit in the center. Keep a close eye on their speed because you have to adjust your lead a lot for it. If they're moving faster than 7 knots, you've got to lead them more, to the point you're not even looking at them through your scope when you fire. At 10+ knots, you have to lead them ridiculous amounts and they can effectively turn on a dime (in a nautical sense) making them tough targets. At 5 knots or less, you can practically shoot it at any point on the ship and it will hit.
Don't forget to drop your own speed at around ~900 meters, so you don't drift too close (causing the torpedo to fail to arm before it impacts), so you have time to adequately plot your shot, and most importantly so the ship doesn't see the ripples created by your attack periscope and change course after you fire.
I've made kills as far out as 1500 to 1700 meters but I couldn't tell you the math I used to achieve it. At that range a single degree change on your scope equals 500+ meters on either side of your target by the time the torpedo gets there.
I've never had problems with tubes just straight up disappearing though. I'd avoid screwing with manually setting the timing on the torpedos. It's hard enough lining up an accurate shot, trying to set the torpedo up to detonate at a fixed point is way too hardcore for me.
Also remember, you have rear tubes and they point to the rear. So trying to fire your rear tubes at a ship in front of you is a waste of ammo.
I don't honestly go in for the manual aiming. There are so many things you have to do right on mark, even with simplified aiming, I'd never attempt it.
So yeah, I just watched your video.
First off, that stuff doesn't fly later on the in the war. You're cruising, at 16 knots, surfaced, toward a ship less than 1000 meters away in broad daylight. They know you're there. And you can see the ship turn after your first volley to avoid it.
Secondly, your angle of approach made it way harder than it needed to be. You were coming in at a steep angle which not only reduces the size of your target, it can cause torpedos to deflect when they strike the target, because the pin on the front of them doesn't smash to detonate it.
Thirdly, you lined yourself up on the dead center of the ship when you fired. You've got to remember you're looking through a magnification scope. When you fired, you were essentially shooting at where the ship wasn't going to be. All it took was a very small course change for him to avoid a tail impact.
90 degree approaches are the best but they take a lot of time and finesse to set up. The pay off is worth it though. Properly lead, a ship that doesn't know you're there cannot avoid being struck broadside.
I had to spend 2 days playing SH3 before I even began to have a grip on the "automatic" targeting system. And when the war actually starts......oh man. You have to play it so smooth. The Radar trawlers, air planes, deck guns on lots of ships and them all being in radio contact means you don't have the luxury of lining up your shots in the open like that, or moving at those speeds. 90% of your shots have to be taken while submerged, which leaves you moving at a paltry 7 knots while needing to flank targets. Which means you need to have a plan that doesn't involve ramming your target. I've spent a full day stalking a ship for the express purpose of getting ahead of it and lining up that 90 degree angle shot. It feels like it should be a lot easier to hit targets in SH3 than it is. I still hold my breath every time I take my shot, I take nothing for granted in that game.
The game really makes you appreciate how much of a fucking magic trick it was for WWII submariners to hit the equivalent of a limousine in floating around in space with a slow moving tooth pick, without the benefit of lasers, computers or GPS.