You put too much faith in me, but looking up “metal gear node nerd” brought me to a Reddit comment quoting from an interview with the translator.

Finally having an inside source on the matter, I ask about the Nerd/Node piece of dialogue in the game. Looking over the original Japanese file shows that ‘nerd’ was written in Romaji (English letters), while above it, in smaller Katakana-based Furigana (which is usually written in Hiragana and placed above difficult to pronounce Kanji), was the phonetic Japanese word for nerd, and then besides this in brackets were the Japanese equivalents, including the word ‘otaku’. Even as a non-native Japanese speaker, the original set-up for this one line seemed awkward. Agness explained, “Regarding node vs. nerd, I do not remember that particularly. However, I do remember a general pattern of attempts to kick it American-style in the original. I felt it was essentially juvenile name-dropping, whether it was ‘hey, I speak English, look!’ puns like this one, or knowing references to mushers and the NSA. The saddest joke is that Japanese nationals who actually know about this stuff - SDF officers, war journalists, sketchy wanderers - would have been amazing sources for an actual writer.”

So it looks like @KobaCumTribute@hexbear.net was right, @doublepepperoni@hexbear.net.

The Japanese Wikipedia article for ナード does not indicate that it is a common word in Japanese contexts, either, basically explaining that nerd is “equivalent to otaku”. So it really does seem like this joke was just an attempt by the game’s writer to flex English skills / Yankee cultural knowledge.