I would glue the knots with thin super glue (depending 0n how tight or loose they are ) or epoxy (slower) and cut as normal. The speed of the cut should be fairly fast and use an upcut spiral bit. The glue just stops the knot from moving or flying out. A tungsten bit should go through knots without too much trouble so long as they are not loose. A good tungsten bit can cut metal so a knot in wood should be no problem.
Cheers
Andrew