…although “Photon Water Balloon” doesn’t sound as cool.
But, as we see, it is not. That’s canon. You can bury a dead guy in one whilst plating Amazing Grace on bagpipes.
The trouble is, they don’t stay dead…
In the first season of Voyager they make mention of having a limited supply of torpedoes. But like all of their limited supply issues, they pretty much ignore that as the years went by.
They kinda give it some explanation early in the series that they trade for materials as they move along (or find needed minerals and mine them as they pass by a given planet). I know replicators are kinda magic but you’d think they can’t make all the things needed but, as you say, they just ignored it in later seasons.
That’s my problem with both Voyager and Enterprise: it’s not so much that they set the parameters with the initial restrictions (Voyager no new crew, no new supplies, Enterprise only can reference things that are correct for the 2150s, like not knowing what Romulans look like) that boxed them in, it’s that they totally ignored them by the first season. How many shuttles regenerated on Voyager in 7 years? 
Back to the torpedoes, in the 60s watching the show, I thought the torpedoes were actually energy bundles
Probably because the limits of 1966 effects and budgets made them look like that. But they made a cool sound. Like the time I walked into a power pole guy wire…
Now you’re just confusing things; hitting a guy wire is how they got the blaster sound in Star Wars.
As long as you remember to cut off the “Ouch! Shit!” at the end of your original recording. 
Unfortunately, I ran into it with my throat. My recording would have been " !"
I saw a YouTube once where they compiled every scene of the Voyager firing a torpedo, along with a running count of how many were left. By the end, they were down to around -173.
Well, if trek is “Wagon Train to the stars”, then the future equivalent of the never-empty 6-shooter is only appropriate.
In principle it sure seems like it would be easy peasy to replicate the things-you already have the antimatter, and if you can’t replicate various parts for the ship you’re probably totally fooked to begin with with no starbases to replenish and repair at.
Someone said upthread that near miss explosions wouldn’t do anything, but even with the caveat that they called them “phasers” in Balance of Terror, torps clearly had that capability then and caused the Romulan warbird quite a bit of damage with their near misses. [Yes I am also aware they used them as analogues to Navy depth charges c.f. the ep being a remake of the film The Enemy Below]
I too want to be on record as thinking as a kid that they were an energy bauble, and was deeply disillusioned the first time they showed one as an actual mechanism/pod thing. So what is causing them to sparkle and shine as they are fired?
Do you know how hard it is to aim one of those things?
Do you know how hard it is to get a photon to sit still?
As I recall, the Technical Manual said they glow because they are surrounded by an overpowered shield that makes them effectively impossible to shoot down. Which at least explains the lack of active antimissile systems.
They would have to be shielded or else you could deflect them with the transporter, or even reflect them back into the ship that fired them.