you can only leave the "stitch" part of the wire embedded if it is/will be flush or embedded into the fillet. If it protrudes it will cause a bump that will interfere with you glassing.

In larger yachts, or thwose boats that are exposed to the elements year round, the wire left in the boats will expand and contract more than the wood/fiberglass and end up working themselves free, and thus exposing the wood to the water, For small boats that expect to be sheltered, this is not a worry.

Ive never had any problems with removing the wires. I cut them on the inside, and use some angled plyers to pull at teh knot end on the other side.