The scientific reason is only this: There are certain compounds of sulphur in an onion. One can fairly call it mild acid. When an onion is cut these compounds spread around in the air and cause eyes to burn. But fortunately they are water-soluble. As a result they dissolve in tears, so after a while the pain ceases.
When the onions are kept in a bowl of water for some time before being cut, these acidic compounds are dissolved outright and don’t spread around. One can avoid eye-burning thus.
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