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You have options. If you are not looking to vacuum the substrate you can cover your hose with pantyhose to keep them out. If you are, you can try to scare them away and go to it. Or, you can go ahead and suck them up and catch them from the container you drained into.
I usually use airline tubing on my 5.5 gallon tank and just keep it away from the babies. The shrimp and snails keep the substrate pretty clean for me.
I use a white bucket. If you swirl the muck in a clockwise direction slowly, you will learn quickly which little darting zig zag moving things are shrimplets.
Holding the tube mid water away from plants you will have less shrimp suck through the tube. Wait a while to do the substrate vac until the majority of shrimp are bigger. Feed less per feeding and feed say 2x per day instead of one. And careful not to over feed!