Ive got cherries breeding in my nano, which doesn't have mollies but does have a fair flow rate. Most probably get sucked into the filter but as TDI says some will probably fall between the plants into areas of relatively safety until they are big enough to fend for themselves.
FYI - I stated with around 15 cherries a few months ago. I counted at least 50 when I stripped the tank down a few weeks back and I not have to feed them more than I feed the fish!
if you can put a pile of gravel in the tank temporarily the baby shrimp will have something to hide in.. it needs to be very course to allow them between the stones but it will work pretty well. The babies will naturally seek out a safe hiding place. this might allow you more survivors.