The oldest reference for “how come” in the Oxford English Dictionary (OED) is an entry in Bartlett’s Dictionary of Americanisms published in 1848. Although the OED calls “how come” an American coinage, the entry in Bartlett’s indicates it originated in England: “Doubtless an English phrase, brought over by the original settlers.”
“How come” is believed to be short for “how did it come about that,” “how is it that,” or “how comes it.”
A web search turned up examples of these older phrases:
Although “how come” is a legitimate substitute for “why,” it’s informal; the OED labels it as colloquial.