99% of the time if you ask 'where are my shoes?' you want to find just a pair of shoes to wear immediately.
So in Indonesian as per http://users.ox.ac.uk/~cpgl0015/indonesian.pdf to refer to a pair of shoes you would not duplicate it, and say 'mana sepatu saya'. But if you were moving home and had a whole box of shoes to find, you might say 'mana sepatu-sepatu saya'.
So the default answer should be 'mana sepatu saya?'