Wx balloons are still used. By the time they get up to the the cruising FLs they're bleeding big (can't recall how big but I remember being very surprised!) but the payload is very small and doesn't weight much. Nonetheless, at cruising speeds I suspect that it could still make quite a dent.
I heard that a risk assessment on the things was done a while back and I believe that the probability of aircraft meeting balloon at high levels was very small - hence it was considered tolerable.