The armies loyal to Takhisis are said to have intended the draconians to die out once the war was won and they were no longer needed- but years after the War of the Lance the draconians led by Kang found a clutch of live draconian female eggs- what were they created for?
In The Doom Brigage and Draconian Measures you get more of the history of the female eggs. The dragons lay the eggs, then the priests of Takhisis corrupt them. In the Doom Brigage article they mention
Multiple draconians are born from a single corrupted dragon egg, with the exception of auraks, with brass eggs producing the most (but weakest) draconians.
If only a single Aurak comes from a gold egg, it suggests the eggs themselves determine the sex of the dragonican, not the evil process that splits the embryo from dragon to draconians.
Unless someone has a link to the books stating otherwise, I'd offer up the theory that originally they used scrying spells to only hatch the male eggs and destroy the female ones to stop the army from breeding out of control. The eggs that Kang & Co found in the Doom Brigade might have been set aside as a plan B, if they ever ran out of actual dragon eggs and needed to bolster the numbers of their draconian army.