Suppose I put a pendulum of metal ball and very thin rope in highest achievable vacuum. What would keep it from not swinging forever?
If this is a real system with a real rope (no matter how thin) attached to some point on a wall, and not just some hypothetical system with 0 friction and such, then yes eventually the pendulum would stop. The cause would be the loss of kinetic energy from friction between the rope and whatever it's attached to. Really, as long as the rope is physically attached to something, there will be some friction.
I think the best bet for perpetual motion would be if the pendulum was held up magnetically, so no physical contact would be needed.