Throwing it in the pool would make it harder to disarm by the police.  Also if the bomb did go off it would cause more damage to the building if it was in the water.  I prefer to think that Sherlock assumed Moriarty might return giving him an advantage by throwing the jacket where he would be standing.

What we know is that the trick worked 4 times before Sherlock.  It is presumed that the other times each person was presented with 100% chance of being shot or 50% of picking the correct pill.  Unless the cabbie lied only Sherlock knew the gun was fake.  The cabbie said he would take 1 of the 2 pills but we never see him take the pill.  Sherlock says he wasn't going to take it but we could see how the cabbie was talking him into taking it.  If both pills are poison that means each person took a poison pill and he would simply leave to let them die, no reason to take the pill.  If the other 4 knew they were dead no matter what why not accept the gun shot making their murderer more likely to be caught, they had to have the illusion that they might not die.  If only 1 of the 2 pills was poison it wouldn't matter which person took it first.  Sherlock should have hidden the jars and represented them to the cabbie to read his reaction.