If an item says:
+1 to spell DC, +2 spell attack rolls and +2 to spell damage
and you cast magic missile, would that mean your magic missile does (d4 + 3) per dart?
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For your example, if a magic item grants 1 to spell DC, +2 spell attack rolls and +2 to spell damage, then due to its wording it would increase spell damage by 2 whenever damage from a spell is calculated. (I would rule that a non-damaging spell would not be affected since it wouldn't have a damage formula to increase or a damage type.) In this example, magic missile would deal extra damage on each dart.
Jeremy Crawford indicates in a question about Empowered Evocation which is similar that you should determine the damage for a single dart and use that for every strike. (Your DM may decide to roll each dart's damage separately, but you should still get to add all of your bonuses to each dart.)
Q: say you have +3 to spell damage from feature. Magic missile 3 bolts. +3 per bolt or flat +3?"
A: Empowered Evocation does benefit magic missile's damage roll.
Q: x per bolt,even on same target?
A: Yep. It's one damage roll, just like fireball, but that roll can damage the same target more than once.
Since this question started out very generically.
The exact wording of the feature that grants the extra damage is very important. If the spell has to be a hit (which requires an attack roll), sometimes a save, and sometimes it just has to deal damage, or be qualified in some other way.
The 1st level Warlock spell Hex adds an extra 1d6 necrotic damage whenever you hit with an attack. So this would not apply to saves or spells like magic missile that don't require an attack roll or a save.
Knowledge Clerics gain Potent Spellcasting at level 8, where they add their wisdom modifier to the damage of any cantrip. This would apply to any damaging spell.
Evocation Wizards gain Empowered Evocation at level 10. This feature adds their intelligence modifier to the damage of any wizard evocation spell. This would apply to any wizard evocation spell, whether it used attack rolls or saves. Magic Missile is such a spell.
1d4+3 Damage each dart but rolled once for all darts.
You create three magic darts. Each dart hits a visible creature of your choice. A dart deals 1d4+1 force damage to its target. The darts all strike simultaneously and you can direct them to hit one creature or several.
+2 Damage to Spell Damage would alter the emphasised part as:
A dart deals 1d4+3 force damage...
Crawford revealed how to calculate MM damage here.
It's one damage roll, just like fireball, but that roll can damage the same target more than once.
So when you cast MM you would roll a D4 and add relevant modifiers, then all darts would deal that much damage to their targets.
For other spells
If a spell you cast deals any kind of damage you should note "+2 damage modifier from magical items" and simply edit the damage.
1d10 becomes 1d10+2, 1d4+1 becomes 1d4+3 etc
Off-topic: Consider talking to your DM before attempting this as 3d4+9 (min:12, max 21 damage) with a sure-hit can be quite powerful considering it's a 1st level spell.