As much as I hate being the "this won't happen" guy, a Muslim Iberia would likely mean relatively little sea-faring by Iberian Muslim polities. The whole idea behind Portuguese and Spanish sea-faring was to bypass Muslim states to get to India. With a Muslim India, there'll still be some use to bypassing other Muslim states (cutting out the middleman, so to speak), but it'll be far less. Which means it's unlikely that the Muslim equivalents of the Portuguese Jesuits will be active in Japan.
Why would they want to bypass them less?
Pragmatically speaking, having direct access is useful.