First of all, I have a degree in electronics. And YES, it can confuse the cruise control, especially in an older unit. The reason is that when the brake lights are off, they look like a very low resistor to ground. Incandescent have a very significant turn on current, so it almost looks like a short. The cruise control wants to see this near short to ground, so that it knows the brakes are off. LEDs do not have a low resistance to ground when they are off, which confuses the cruise control, preventing it from turning on. The solution is easy, one just needs to add relay to the brake light circuit so that it really sees the off condition.
As far as the flasher, any auto parts store has a solid state flasher unit that plugs into the standard flasher relay, and will make the blinkers work correctly, regardless of the load.