I would guess that with the internal filter, there is going to be a good chance that any baby shrimp that get too near the intake may end up sucked into the filter...
A sponge filter would most likely work better to avoid shrimp getting sucked into the filter, or maybe you could try adding a patch of moss in an area away from the filter intake for the babies to find refuge in... that imo, MAY help, but still can't guarantee that it won't suck any of the baby shrimp in due to their small size...