Edit: my first thought in this post is wrong, please see my example in the post below it
Ah, thanks. It's probably this issue...
https://www.stat.berkeley.edu/~s133/factors.html
"To exclude certain levels from appearing in a factor, the exclude= argument can be passed to factor. By default, the missing value (NA) is excluded from factor levels; to create a factor that inludes missing values from a numeric variable, use exclude=NULL"
sorry, I was wrong. I think the thing to do, is not bother with naming NA factor level, just name your other levels, when you go to do the table though, use the helper function addNA