What my gf and I found was that we like the plug the holes in our Perception Prism SoT kayaks on cooler days, but unplug them on the really hot Florida days to use the feet-area water to help stay cooler.
Too bad the Prisms are just about useless as a dive kayak...
Plugging the holes will raise your center of gravity, making them slightly less stable. This is almost unperceivable, but it will be dependant on your hull deisgn and water conditions. Too, since I don't have a rod holder, I would stick the end of the spinning rod into one of the holes to take a break, or try trolling, sometimes.
On that note: Some kayaks are actually stable enough that, on calm water, a balanced person can stand up on them, mid water, to take a better look around. I've done this just to test out my balance and my 'yak. What I haven't done, but what was implied by some kayak salesman to me, was that there's at least one kayak he could stand up and cast from. I don't think I'll be trying that.
Remember: when the alligator bites your paddle, hold it loosely, he'll probably let go.