Thanks to Matthieu for the email.
require(data.table)
DT <- data.table(v1 = c(1,NA,2), v2 = c(1,NA,2))
DT[!(v1==1)]
# v1 v2
#1: 2 2
DT[!v1==1] ## different result due to auto indexing
# v1 v2
#1: NA NA
#2: 2 2
options(datatable.auto.index=FALSE)
DT[!v1==1] ## turning off restores default functionality
# v1 v2
#1: 2 2
Thanks to Matthieu for the email.