Anyone where the "ou" romanization for long o vowels comes from (e.g. 少年 being rendered as "shounen" rather than "shoonen" or "shōnen")?

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Wikipedia suggests it might be from Wāpuro rōmaji, where "u" is always used to spell the kana "う"

Wikipedia is right; the romanization is just matching how it's rendered in kana.

Because 少年 in hiragana is しょうねん: spelled out that is "sho u ne n"

Many, but not all long vowels in japanese follow these:

ああ a i -> as in おかあさん, mother

いい i i -> as in ちいさい, small

うう u u -> as in すう, to smoke

えい e i -> as in せんせい, a teacher

おう o u -> as in こうえん, a park

Yes, exceptions to this exist (like おお) and some are actually dipthongs and not actually long-vowels, but easier to think of them like that.

Look at the standard kana table: https://en.wikipedia.org/wiki/Goj%C5%ABon