I think we've covered this before too.
It seems that, logically, there are more than one Legendary Pokémon, they are just seen ever so rarely. If there was only one, who would take over the role of the (for example) Lugia, when it was caught? They have to have some way to have offspring, whether it be an egg or some way to duplicate themselves. Or maybe something like the way some animals can change their gender when there are none of the gender left, legendaries might have the ability to produce offspring when the time is needed.
It seems that, logically, there are more than one Legendary Pokémon, they are just seen ever so rarely. If there was only one, who would take over the role of the (for example) Lugia, when it was caught? They have to have some way to have offspring, whether it be an egg or some way to duplicate themselves. Or maybe something like the way some animals can change their gender when there are none of the gender left, legendaries might have the ability to produce offspring when the time is needed.