Do you mean puddle? Puddles are generally (unless hiding a pothole on the street) too small to hide a crab - perhaps you meant pond (or tidal pool)?
Use "The crab will not appear (or will not come) if you throw rocks" if you know there is only 1 crab in the puddle and want to see it.
If you do not know how many crabs are in the puddle:
Use "The crabs won't come if ..." or "Crabs won't come if ..." if you hope any number will come or you wish to emphasise the action of throwing the stone.
Use "A crab will not come if ..." or "No crabs will come if ..." to emphasise you won't get to see any crabs.
Edit (to answer the questioner's comment / further question to this reponse):
You have to use the article "the" in the mother's response: "No crabs will come if you throw stones in the puddle". You would never omit an article - "No crabs will come if you throw stones in puddle" is never used.
If you say "No crabs will come if you throw stones in a puddle" you are either talking about the abstract concept of crabs and some general theoretical puddle somewhere (not likely that a small boy would be having this discussion) or talking about a puddle you are at that is (potentially) miles away from any crab and that you hope/expect that by not throwing a stone in the puddle, some random crab (why not a lion) will come walking along and you will see it.