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Nope. RStudio encrypts your credentials (using a JavaScript RSA implementation) It is possible to run RStudio server behind a proxy or over ssh tunnel instead (e.g. with all other ports behind a firewall) for additional security; see the RStudio documentation.
We started out by providing both Ubuntu and Debian versions of each of the Docker images. After further testing, we decided this was unnecessary and would simplify things by providing only Debian-based images.
If you are just running the images as-is (rather than using them as a base for your own Dockerfiles), there are very few differences between the Ubuntu and Debian images. The Debian images tend to be smaller, particularly for the simplest images like r-base or rstudio. Focusing on just Debian makes our work a little easier and puts less stress on the build infrastructure. Docker best-practices recommends Debian and many official base images build on Debian.
Docker excels at modular reuse. If you intend to build upon these Dockerfiles, we suggest you choose the flavor that matches any other configuration scripts you might want to (re)use in building your extension -- for instance, if you already have your project running on a Debian machine, that makes the most sense. Conversely, if you've written a .travis.yml for your project, the configuration is likely to match the Ubuntu images most closely as Travis runs on Ubuntu. In our experience many scripts will run equally well on either flavor.