It depends on so many factors that there can't be a single answer. The main point to consider is that a lot of water in the cockpit or elsewhere on any SOT will make it unstable. If you can reach the plugs then you can leave them in and only pull them out if it fills. I'd be very uncomfortable plugging anywhere that you can't reach.
I have an Adventure. Because I'm light, my coxkpit stays perfectly dry. If you are heavy then you have a prmanent wet bum. I have scuppers under my seat. If I remove them I will have a wet bum. If I leave them in then I get a maximum of an inch or two of water in that small area, with the rest draining through the Mirage scupper. I can unscrew these plugs to drain most of the water if I get swamped.
The ideal solution are venturi scuppers with a one way valve. These will drain a moving kayak but prevent the water coming back up when stationary. Best of both worlds.
Here's a great idea from Spooky.
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