I've concluded it's first come, first served. Your first empty slot will get the torpedo highest in the reserve queue.
So, if you fire a salvo of bow slots 1 and 3, slot 1 will be filled by the torp in bow slot 5, and slot 3 will get filled by bow slot 6.
Since I rarely fire salvos, I try to take the reserve queue into account when deciding which tube to use, so as to keep a mix at hand, but it's generally random by the time I am down to 3-4 forward torps.
Of course, in the back (on a VII), you really have no choice at all.
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"Well, now, that's true... the IXC is a bit of a chick magnet..but you really can't beat the VIIB for off-road fun."
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