It sounds like your Alert time of the day is 24 x 7 but you email alert action Time of Day is 6AM to 6PM. You may want to change the Alert time of the day alone to 6AM to 6PM and don't set any specific time of day for the email alert action. This will notify of devices that are detected as down or come back up between 6AM and 6PM. As superfly99 suggested, you may want to copy the default node down alert and leave the 'log to netperfmon' actions so that you know when devices go up or down in the historical Events but remove the email action for the out of the box alert.
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