That really depends on your comfort level. Do you have a surge supressor on your house? Can you afford to lose the pump if lightning hits it? How likely is lightning in your area?
Having said all that I leave mine normally connected to the timer. If it's on, it stays on. We live in an area that doesn't have many issues from lightning storms.
The pump is pretty far down the list of things likely to be damaged by lightning. Sure, a pump can be damaged by lightning, but that isn't especially likely. It is much more likely for a SWG or automation system to be damaged. And turning everything off doesn't completely protect it either.
Over the years I have lost all sort of things to power surges and lightly strikes (including direct hits that blew out copper plumbing pipes), but never a pool pump. Instead it seems pump motors tend to die from corosion issues.
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