DT <- data.table(iris)
system.time({
  for (i in seq_along(DT)) set(DT, sample.int(nrow(DT), sample.int(nrow(DT) / 10, 1)), i, NA)
})
# user  system elapsed
#    0       0       0
sapply(DT, function(col) sum(is.na(col)))
# Sepal.Length  Sepal.Width Petal.Length  Petal.Width      Species
#           12           11            6           11           12