That's an interesting idea -- I've heard the word "америкос" but I didn't think about it as a possible source for "пиндос".
After some Googling, I found that there's yet another theory that I hadn't heard before: The Spanish word pendejo (пендехо) is popular slang in the American military, even among soldiers who don't speak Spanish. (It means дурак, although the more literal meaning is "a pubic hair"!)
Although it's extremely unlikely that "пиндос" was in any way borrowed from pendejo, it's possible that the widespread use of the Spanish word by U.S. soldiers increased the popularity of "пиндос" among Russians. One can even imagine such a conversation taking place during the Kosovo war:
AMERICAN: Privyet, pendejo!
RUSSIAN: Хэлло, "пиндос"!
English-speaking linguists would say that "пингвин + америкос = пиндос" is an example of a "portmanteau word" (слово-чемодан) -- a term invented by Lewis Carroll in Through the Looking-Glass.Just sort of "phonetic transfer" (I'm not sure it is a correct term or not).