The reason the outer skins are thinner is so that the ply will have even strength and flexability in both directions (there is the same amount of wood with grain running in both directions). If all plies were the same the sheet would be be very stiff across the grain of the outer plies and very flexible along the grain. So if the outer plies are 1mm and the inner ply is 2mm that is perfect. The only problem is that if the outer plies are too thin you could easily sand through them and produce weak spots on your kayak.
The species of wood used in making the plywood sheet is not of great importance as long as it is completely covered in epoxy although some woods do soak up epoxy better than others. The wood used in most marine plywood would not last long if not protected so there is nothing too special about it.
It is most important that the glue used is waterproof (it should be black) this will prevent the kayak falling apart if there are any breaks or deep scratches in the epoxy but these should be repaired as soon as possible to prevent the wood from rotting.
As others have said it is the quality of the wood used in making the plywood sheets that is most important this will ensure that there are no large voids in the sheet and the outer plies have nice looking faces.
So you should have no problems just be careful when sanding and make sure everything has a nice coating of epoxy.

Jon