Nobody cites every package they use, it's not feasible. I use a lot of packages, and some journals have a limit on the number of citations you can have. I only cite packages when it provides specialized statistical functionality.

For example, I do a lot of work with data from complex surveys, and I always cite Lumley's survey package because without it I wouldn't be able to do the work. On the flip side, I use Hadley's readr package extensively because I think his I/O functions are more sane than the defaults. I'm not going to cite readr in every paper I write just because I'm too lazy to type stringsAsFactors = FALSE when I read a csv file.