Sure, there is conception now, but we're likely dealing with traditions and taboos laid down before such things we're common. Theocratic regimes arent big on admitting rules change due to time and technology.
Also, forced rape does many things, such as potentially damage a womans ability to reproduce through physical trauma and STDs. Ruin one fertile young girl's uterus and you've taken money out of a Holder's pocket, quite a lot actually. Im sure there are "pleasure brigades" for overseers and such, but I doubt they're allowed free reign of the slave stock. (though rape as a threat and a punishment is possible, and likely a compelling one)
The fact that the Amarrian place such a high import on their own genetic identity ("we're the chosen people of God!"), and there is a recognizable Amarrian bloodline at all after centuries of conquest and enslavement means that breeding and mixing of blood with "lesser races" seems to be a very uncommon event. Otherwise they wouldnt even be recognizable as a distinct ethnicity after centuries of taking concubines and such (in contrast to the Romans, who fucked anything, and didnt really exist as a recognizable, distinct ethnicity after a few centuries of Mediterranean hegemony and empire )
And if the Amarr dont do it, I doubt they let the races they're trying to teach to be more like them do it.
EDIT: but, the footnote you cited does challenge this idea a bit. That said, my first point stands.
Further edit: Im defining rape as forced sex, a violent act. In practical terms, im defining it the way most IC backgrounds define it really, which is what Esna mentioned.