Should I cite all R packages I used?
YES.

There are lots of reasons to and no reasons not to (unless you're under some kind of strange space/ink constraint). 

Here is an important and underappreciated reason why:

Most of the people who make the kind's of R packages, in fact the people who made R itself, are other academics. Meaning: They didn't get paid specifically for the time they spent making lme4, ggplot2, stargazer etc. Software development is very unappreciated in academia. Imagine spending a lot of time writing and maintaining a package that is used by thousands of people in your field and then being asked by a tenure/promotion committee why you didn't write more papers or do more experiments. It's very difficult to get someone who isn't a user (or even a software-minded person) to properly appreciate the time and skill involved in making good software. 

The only way to convince university systems and leaders that the work you spent writing that software is to show them in a way they understand, that means citations. They're not going to care about your StackExchange reputation or how much juice you've got on github, they need something Scopus can compute and they can itemize and count.

Much of the workings of academia is based on beans. Much of the effort at universities is dedicated to counting and managing those beans. How many students are in your program, how many grants are awarded, how many Ph.D. defend, and how many papers are published and cited are all very important beans which decide who gets resources. It would be sad indeed if someone who wrote a useful R package didn't get the credit they're due and thus be allowed to make more wonderful tools. Imagine if Hadley hadn't started working for R-Studio, he might be standing in front of some committee someday asking him why he spent so much time writing "software" instead of "papers," or trying to explain why he can't take on a third course this semester because the dept chair doesn't understand that writing software is something that actually takes real time.

Also consider this:
Most scientific papers are cited fewer than 10x, if ever. A reasonably useful R package is likely to impact many more people than any "real" publication, but that person get's no credit if you don't cite it.