You can remove the wires.  Just snip the wire flush on one side and heat the other side with a lighter or some other heat source for a few seconds and the wire should easily pull right out with a pliers.  Don't heat too long, or too near the hull or you may singe the wood.

 Enjoy your build!  Mike

a little propane torch like the plumbers use works well if you turn it down real low and exercise a little caution to not get too close to the wood. You'll have those wires out in no time.

Erik,

I like the idea of removing the wires and sanding down the fillets, especially since I don't have to be the one doing it, but just for completeness here's a couple of other options:

1. You can definitely put another layer of putty over them. System 3 refers to that as cosmetic filleting. The downside is that you'll use more epoxy and woodflour and your boat will weigh more than it would have with thin fillets. The upside is that you won't need to fool with the wires and potentially dangerous heat sources. You'll also end up with easier sanding, especially if you smooth out the fillets by lightly brushing them with unthickened epoxy while they're still soft. Since this is a trailer boat anyway, the weight may not make any difference to you.

2. If the fillets are somewhere that's going to be painted,leave them alone for now. Once you get to the painting prep, fillet over them with a stiff mixture of epoxy and phenolic microballoons (available from CLC). The cosmetic fillet will then be much lighter, use less epoxy and be way easier to sand. The downside is that it's a butt-ugly purple color that really screams to be covered in paint. But if you're painting anyway, no problem.

Finally, if you decide to go with the wire removal, use a flameless heat source like a soldering iron. Open flames in a shop full of solvents, paints and petroleum products, as well as wood and sawdust is probably not a good idea.

Good luck,

Laszlo