sum(is.na(ffdf$columnname))

lapply(ffdf, function(x){sum(is.na(x))})

$virtual
[1] 0

$physical
[1] 0

$row.names
[1] 0

require(ffbase)
myffdf <- as.ffdf(iris)
lapply(physical(myffdf), FUN=function(x) sum(is.na(x)))