A large enough fish could cause you to flip your kayak but it's usually a rare thing that happens.
If you're a beginner with Kayaks the sit on top Kayak is better and for more experienced Kayakers the sit in is better especially if you're in cold or rough water and don't want to get wet.
The sit-in kayaks perform better than sit-on-tops.
There are several reasons for this: Your center of gravity is lower, which allows the kayak to be narrower and still maintain stability.
A narrower kayak moves through the water more efficiently than the wider sit-on-top.
Sit on Kayaks have holes for 2 reasons which are to act as a drain and to also add structural integrity to the Kayak.
These holes on Kayaks are known as scupper holes.
Scupper holes are intentional holes in sit-on-top kayaks, like fishing kayaks.
It seems counter-intuitive to have holes in a boat, however they serve a couple important design purposes: They help give structural integrity to the kayak…
They operate as a drain hole when you get water in your boat.
Scupper plugs are only applicable for kayaks that have scupper holes.
Without scupper holes, there is simply no need for scupper plugs.
It's important to remember that scupper holes are included in sit on top kayaks for a reason.
They are an important safety feature and highly recommended for beginner kayakers.
A sit-on kayak is basically an air-filled plastic float and the scupper holes allow water to pass in and out of the kayak without allowing it to sink.
With this design the paddler sits up off the water as well.
For all safe kayaks, the standard number of scuppers is four holes.
The holes are designed to ensure that water drains off the deck every time the kayak is at a standstill.
Many kayaks are crafted with innovative hulls to ensure that safe-bailing can happen without the need for forward movement.
Sit-on-top (SOT) kayaks are nearly unsinkable under normal circumstances.
The most common way to cause your sit-on-top kayak to sink is to ignore the weight limit of the vessel.
Even then your kayak will stay mostly afloat, but will not allow you to ride it.
A sit-on-top kayak should never truly sink.