Zapolya would still claim the throne, less succesfully than IOTL-Sigismund would not support his claim over *Louis III*.
Another question: thrones of Bohemia and Hungary are elective, and Ottoman invasion is not the best time for kid on the throne. Wouldn't Ferdinand run for the crown himself, just promising to name baby Louis his successor? Or he'll be choosen to be "temporary king", like Vladislaus of Varna, who promised to abdicate Hungarian throne once Ladislaus the Posthumous reach majority (another question is, if he'll really do it when that day came)?