There's nothing wrong so far as I'm aware of inbreeding with invertebrates. It doesn't seem to be so much of an issue as it is with say, mammals (otherwise feeder roach colonies wouldn't last very long). You can also do an exchange with other hobbyists every few generations to keep your scorpions' gene pool well-mixed.
In the wild emperors live in large family burrows, so I imagine inbreeding is quite common in those circumstances.
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