Death by many Magic Missiles
Let's start with when to make Death Saving Throws (PHB, 197)
If you take any damage while you have 0 hit points, you suffer a death saving throw failure.
So any time something gives you damage while at 0 hit points, you suffer a saving throw failure.
As quoted above in the question, the language for Magic Missile is separate per missile. Each missile strikes simultaneously, but the damage from each is separate. If we are separating damage, we are separating those Saving Throw failures.
The Concentration function is similar in that it triggers off of damage (PHB, 203):
Whenever you take damage while you are concentrating on a spell, you must make a Constitution saving throw.
However, it also goes on to state:
If you take damage from multiple sources, such as an arrow and a dragon’s breath, you make a separate saving throw for each source of damage.
Jeremy Crawford specifically ruled on Concentration saves and Magic Missile requiring each missile to force a new save.
Roll for each missile
The real question
That leaves us the real question here as to whether or not Magic Missiles are separate sources of damage, or if the missiles hitting concurrently represent a single taking of damage.
Given that Crawford seems to believe that magic missiles are multiple sources that require a roll per source, it seems you can extrapolate that the missiles are also giving damage separately (while hitting concurrently) and thus forcing death save failures for each magic missile. The concurrent nature of the strike doesn't override the multiple deliveries of damage from separate sources.
Caveat Emptor
If you are a DM and planning to target a PC like this, you must beware of hard feelings at the table. Typically death saves are a PC thing, and if you are going to remove that by going after unconscious players then the possibility of hurt feelings is real. Most monsters are more concerned about taking out other creatures who are alive rather than double-tapping any downed creatures. If there was a real reason by the NPC to do this, then that's different - but if you're just going after unconscious players because they're easy targets to completely kill you may suffer backlash from your table.
Best Answer
No, spells from magic items aren't upcast unless they specifically state it. From the DMG, page 141:
In particular, the description of spell scrolls does not say otherwise.