I'm trying to make sense of this project, but not having much luck. It sounds like you're gluing up pieces of wood to make a panel, then slicing it up into thin strips again. Am I missing something here? Why not just use a saw to cut the boards into thin strips - because you have a CNC machine but not a saw? Why glue the boards up into a panel in the first place? Are you trying to make curving pieces of wood that wouldn't fit in a 6" board? And you don't have a bandsaw?
One thing I can say for sure - yes; if you've got a big knot in a piece of pine 1/2" thick, this will be a problem. A tiny knot, not so much.