Something like this ?
rosterSample <- data.frame(RSHIFTSTART=c('00:00:00', '01:00:00', '00:00:00'), RSHIFTEND=c('10:00:00', '00:00:00', '00:00:00'), stringsAsFactors=FALSE)
ind <- with(rosterSample, RSHIFTSTART=='00:00:00' & RSHIFTEND=='00:00:00')
rosterSample$RSHIFTSTART[ind] <- NA
rosterSample$RSHIFTEND[ind] <- NA