The N29 gets 18bph on Fri/Sat nights on the inner section (Trafalgar Square - Wood Green). Every third bus goes on to Enfield. On other nights it's 8bph throughout.
I think in terms of passenger numbers it's the 25, but in frequency it's the 38 (28bph AM peak typically, but 35 leave Hackney Central between 7 and 8am).
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Thinking about your question again, it's quite difficult to do like-for-like comparisons because a lot of the night routes run far further out than their day equivalents - so the N38 operates between Victoria and Clapton, but continues to Leyton and Walthamstow and carries a fair amount of traffic unique to that section of a night. with the N29 it's easier to seperate because so few buses go north of WG on a weekend.
I think the N29 and night 25 are the only routes that run (sometimes) at a higher frequency than their day equivalents, though I'm open to correction on that.