Not a Shadowdark referee, yet. But long-time OSR/NSR referee and player.
The legalistic answer is there’s nothing in the book about needing to see your target generally, nor is there anything in the spell specifically. So “go for it” is a perfectly fine answer.
The section on darkness suggests disadvantage for tasks requiring sight. So maybe negate the auto advantage with magic missile. Or replace it with disadvantage.
It’s open to interpretation. Like most things OSR/NSR.
So to put the question back on you, what kind of table do you want to run?
Decide based on that. Do you want to encourage legalistic arguments about the rules, go with that. Do you want a more easy going approach, go with that. Do you want to push verisimilitude, go with that. Etc.
It can be frustrating at times, but this is part of the point of the playstyle.
It’s your table. Make a call.
Just be aware what you decide will encourage certain choices and playstyles from your players.