Titles matter more, particularly when they've played in 3 finals against each other, and Nadal has won 2 of the 3. Pretty simple.
Yes they do mean more. But not infinitely more...otherwise making the final means nothing....and we have already established that that isn't the case. The ATP recognizes that winning the titles means 2000/1200 more than the final ie 67% more. But that has been factored in in the calculation.
Repeating calculation post here:-
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Final have bigger factor than 0. Much bigger.
In fact we know exactly how much they are worth - the ATP tells us.
Let's take it away from personal opinion. Let's just measure it objectively on the hard data ie the specific US Open results.
Slam wins are worth 2000 points and Slam finals are worth 1200 points. Therefore making a slam final is 1200/2000 ie 60% of winning a Slam. Semi's are worth 720 points.
Hence the top five results for both players at the US Open are:
Nadal - 2 Wins, 1 losing Final, 2 losing semi-finals = (2000x2) + (1200x1) + (720x2) = 6640 points
Djokovic - 1 Win, 4 losing finals = (2000x1) + (1200x4) = 6800 points
So very close, but Djokovic ahead by a nose.
(We could look at the top 6 or top 7 performances instead of top 5 - but Djokovic is ahead on those counts as well).