Replacing window panels

Bay window and the plywood panels need replaced (worse than the photo shows) so have a few questions.
Any plusses or minuses replacing the 3ply with 5ply as I would see it as a minor security enhancement with 5 ply?.
The existing panels have leaked water and stained the curtains, should I bed the new panel in a thin bed of sealer?
What are the correct panel pins to use to nail the surrounding beading so that there is no future rust staining?

I would recommend replacing the window and the timber, with a full height window. Just done a whole house, looks fantastic.

Ed