I move it around a lot so I always use shut down. Sometimes I forget and use the power button on the console so it goes into standby mode. It complains when after I have unplugged it from standby mode, but it doesn't seem to harm the system.
I see no reason for standby other then to charge a controller. Updates download and install very fast, and cold boot seems as fast as waking up from standby. It takes my projector almost a minute to warm up to full brightness, by then updates have already been applied and the game is running from the last save game.