You could stain the strips, but you will end up removing most or all of the stain when you fair the hull.  Building a strip-built kayak requires even more sanding and some planing than a stitch and glue.  You have to make several dozen or so flat surfaces into one smooth round surface.  I would skip the stain unless you were to use it after fairing the hull/deck.

Stain comes with several different vehicles. You can't use stains with an oil base. They will interfere with epoxy adhesion.

Staining wood is a ticky business, especially on softwoods. It's hard to get consistant results. And, if you ever have to make a repair that requires sandind the wood, it will be difficult to touch up the stain so the repair will not show.