Once the interior fillets and glass have cured, you will remove the wires by untwisting and pulling out with a pair of pliers.  If you have a wire that won't pull, you can heat it with a soldering iron which will soften the surrounding epoxy.  No big deal if the wire beaks off.  Just sand flush with the hull and it will all but disapear.

When you fillet the seam, you are gluing the two pieces of wood together and forming a nice radius for the glass which you will lay overtop.  When the seam gets flat, the fillet does not really do anything except fill the small opening between the panels.  Most of the strength will come from the glass.  In those areas, there is really no need to add enough fillet to cover the wires.  From an appearence perspective, you need not be overly concerned because those areas of the boat will be hidden under the deck.  Another approach would be to use either CA glue or strong tape (on the outside) to hold that area together and remove the wire prior to fillets.