I recall hearing somewhere that the way arthropods reproduce (pumping out a ton of young all at once), the genes get shuffled around in such a way that the siblings aren't as closely related as siblings in say, humans, would be.
I don't know if that's the case or not, but what I do know is:
-- People have bred the same line of roaches for generations with no ill effect
-- When weird mutations do show up in such lines, it can usually be traced to a dietary deficiency
-- Some insect lines in culture have just "dried up" and quit reproducing without an obvious reason (personal experience)
-- No one that I'm aware of has bred the same line of emperors long enough to find out what will happen
That last one is mainly because emperors are so slow-growing. Hopefully someone on here has experience with bark scorpions (also communal, but with a faster generation time) and can shed some light on what happens to a closed gene pool in that case.
(Kejser, I'm looking at you and that B. jacksoni farm of yours.)