Side stepping the arguments about nukes and nuclear warfighting (yes this is a phrase actually used), part of the problem is that the Hiroshima is so often used as a measurement for a weapon or event because its the largest event of destruction in the public conscious so for narrative convience writers will often use such event to tell the player how big the threat is.Soviet Heavy said:Settings like Mass Effect, or Warhammer 40000, will use Nukes as a unit of measurement to try and sell you on how great and awesome the power of their weaponry is. And it is meant to be shown as cool. "Whoa, that ship's gun fires shots three times more powerful than the Little Boy? Wicked!" That's what we're being told, not "Dear god, this is a weapon of mass destruction greater than the most infamous weapon in modern history, and we are making a joke out of it."
However there is also the fact that in real life, space warefare is going to be just a leathal. If you acclerate an object of sufficant mass to sufficent speed it is going to hit with the explosive yield comparatble with nuclear weapons (1KG at 75% of light speed is going to give you a 11 Mt impact). So when mass effect and Halo and other universes throw around these numbers they atleast have a reason to do so. Would such a future be terrifying? Probadly but as we've yet the experience it on any great scale we can't visualise it so we fall back to using Hiroshima to compare it.
But of course we play these games for entainment and so often these games do not so the consequence of such weapons not only people it does not fit with the pacing or plot but also because the resulting images would not sit well with the console owner looking for something to unwind. This is compounded by visual media (TV, Film, Games) often shrinking the scale of space combat and its explosions to fit everything on the screens. According to the lore the photon torpedos on Star Trek have a 1 Mt warhead yet on screen they look like normal missilse.
All of this however has the effect of making many people desensitizatied to the effect of nuclear weapons since they keep seeing them having less effect in the media, that and the end of the cold war mean many people do not understand the effect of nuclear weapons. However this can also lead to the overplaying of the effects of nuclear weapons. Not to go into it but while the effects of the nuke denonation in Terminator 2 are realistic, it still gets the detail of scale all wrong. Not way the airblast could hit Sarah from a ground zero in central LA assuming she's in somewhere like Malibu. Not unless we're getting into the 40+ Mt weapon range.
On the case of Warhammer 40K its a bit more complicated. While on the surface Extermanatris (the destruction of a planet) looks like a immature "OH Wow we can blow up Planets AWESOME!" idea. Orginally the setting was more of a black comedy in which the setting creates an environment where the worse aspects of humanity (facism, extremism and hatered) are needed to survive. While this black comedy aspect has been lost to some extent, in this light the ideas of Extermanatris is more an example of mankinds brutality but also the cruel logic used to justify it.