Do "flat" hands devalue a 4-4 trump fit?
Two separate questions:


Should N have bid 3NT straight off the bat? In my opinion, yes, at any form of scoring, for the reasons you mentioned, and also to conceal information about N and S's shape from West (think about how much easier the lead is after a Stayman auction than after 1NT - 3NT).
Given that N initiated a Stayman sequence, should S have developed a sufficient picture of N's hand to figure out that 3NT was the best spot anyway? No. From the auction, as far as S knows, N could have any number of spades between 0 and 3. (Experienced partnerships will probably have a way to show spade shortness here, by way of showing long minors, but doing this on middling hands that are likely to wind up in 3NT anyway is again a mistake, giving too much information to West.) Even if S could know that N has 3 spades, he still knows that N chose to initiate a Stayman sequence and should respect N's opinion that N's hand has ruffing values. (S has no information about shape that N doesn't have.)