Linq to Dictionary<string, List<string>> with Null values

Why would you expect that in the first place? You're literally telling it to just select value. Neither cultureId nor your Languages array are even mentioned or utilized, so why would you even expect them to somehow play a part?

You'd need something like the following GroupBy:

.GroupBy(g => g.key, (key, items) => Languages.Select(lang => items.FirstOrDefault(i => i.cultureId == lang)?.value))

You can do some join with your languages list, something like this (untested yet)

Dictionary<string, List<string>> query = Translation
    .GroupBy(o => o.key)
    .ToDictionary(g => g.Key, g => 
        Languages.Select(l => g.FirstOrDefault(x => x.cultureId == l)?.value));

Explanation :

We map the group on the list of languages. For each langage, if a matching element with cultureId is in the group, use that value, or instead use null.

(can't test right now, pardon me in advance for any error)

You try to do a "left join" in linq, that is possible using Join and DefaultIfEmpty operators. As long as I know this only can be made on a declarative syntax:

var query = from trans in Translation
            group trans by trans.key into transGroup
            select new
            {
                transGroup.Key,
                Values = from langId in Languages
                         join trans in transGroup on langId equals trans.cultureId 
                             into joint
                         from trans in joint.DefaultIfEmpty()
                         select trans?.value
            };

var values = query.ToDictionary(x => x.Key, x => x.Values.ToList());

I agree it's not the most readable query and maybe it would be simpler to maintain doing it on a procedural way.