As others have said before,
I would agree that an intensified magic missile could benefit from two additional missiles. And per the wording in "Surprise Spells" class feature of the arcane trickster, sneak attack damage absolutely does apply to a damage spell (which magic missile is) if the target is flat footed.
However, this is a separate ability from the normal sneak attack mechanics. That's why it works without the ranged attack roll being required. I agree that the wording is a little vague. If anything, this should be addressed in the next errata. But for a spell that splits up its Total damage amongst multiple missiles, I'd rule that the caster has to also split their Total Sneak Attack damage against multiple missiles, though I'd give them their choice of the split. When I re-read the wording for the Surprise Spells ability, this approach still seems quite fair to me.
In short, my argument is that magic missile -spell- damage is not 1d4+1. It is 1d4+1 per two levels to a max of 5d4+5, which can be divided out amongst multiple targets. I would treat sneak attack damage the same for this type of spell: 7d6 damage, which can be divided out amongst multiple targets. If they hit 5-7 different targets, I would Not give them their full sneak attack damage against every single one, because I don't think that approach is consistent with the spell's own mechanics.
The ability doesn't make a ton of sense, but its a game, so it doesn't have to. It doesn't have to be balanced either, but its a game, so it really ought to be.