Rob: Have you considered tiny sponge filters that have lift tubes?
One of those could work. Would allow you to direct any bubbles to the surface instead of having them plow through the water to the top. There'd still be a tiny bit of flow but it may be more tolerable for the shrimp.
They're probably just getting comfortable with their new home and nature is taking its course.
If they were breeding regularly in their old home, they're probably doing the same in the new one. Since females have to molt in order to breed, that's like what's happening (unless there was some other environmental trigger). They've got tons of new space to fill up with baby shrimp.
You could use just the sponge filter. Since the outflow can be easily extended, you could make it work. With the air flow metered down, you can position the outlet at the water surface and have very little disturbance.