Question: Why did Voyager seem to have more photon torpedoes than the number of photon torpedoes they said they had?
Question: Is there any technology featured in Star Trek Voyager, or other Star Trek series for that part, that seemed futuristic in the late 20th century, but are now reality?
Answer: If you include the original Star Trek series (1966) then there are several. The communicators used in the original series were before (and said to inspire) mobile phones. We currently do have teleportation technology but it currently only works on things the size of a few molecules. A "Cloaking device" also exists; it's a fabric that bends light through it, though it currently only works in infra-red. The Hypospray is real and was patented in 1960 - six years before the original series aired - it's actually called the Jet Injector. Faster Than Light travel is still a few decades off, but there are several real-world theories that look promising, including one that is remarkably similar to the method used in the Star Trek Universe called the Alcubeierre Drive that involves manipulating spacetime ahead and behind the ship and the ship "riding" it. Medical techniques and technologies have also advanced considerably; prosthetics particularity and we routinely have robots performing surgeries where absolute precision is needed. The "Shield" used in the series have a few primitive versions around. The Phasers used in the series are used but are not very powerful (nor will they ever be as powerful as the Star Trek version the laws of physics gets in the way) but rail-guns (using magnets to spin then propel a projectile) and particle accelerators like the Large Hadron Collider have been around for a while. The Replicator would require a nuclear fusion reactor and a nuclear fission reactor in something the size of a large oven and the Holo-deck wouldn't work at all based on our current understanding of physics so those are both still science fiction at the moment, but who knows!
Question: Why did the Borg look different to how they appeared in TNG?
Answer: In universe, the Borg are constantly adapting new technology and upgrading themselves. In reality, they look different because the costumes were redesigned for the higher budget in Star Trek: First Contact.
Question: Throughout the entire show, why is Harry's rank an ensign? Janeway has been seen promoting or demoting other crew members, so why doesn't she promote him?
Answer: In Season 7, Episode 19 "Author, Author," Harry's parents outright ask him why he hasn't yet been promoted. Harry replies, the ship is operating without a full complement of staff, and there is little opportunity for him to be promoted. This, however, was likely added to the script to address complaints fans and Garrett Wang himself had about the character never being promoted.
Answer: For the first 4 seasons they kept to the number originally stated and often referred to the number remaining, however by season 5 it was too much of a writing constraint. It is just assumed that they had found somewhere to replenish their supply.