RTC to DNG links visibility in DNG is strange

Nothing is really wrong and you just need to understand the difference between a "module artifact" and a "base artifact". In your case, the one with the Implemented By link is the module artifact, and the one with the Affected By link is the base artifact. It is a bit confusing as they look the same, but if you check the resource URI, you can see that they're different. Also, if you expand the Overview section, you can easily tell which one is a module artifact (with module information shown in the section), and which one is not (without module information). The easiest way to solve this confusion is select the "include links, tags and comments from the base artifacts" option - the first icon in the top right menu bar. For more information, see
https://jazz.net/help-dev/clm/topic/com.ibm.rational.rrm.help.doc/topics/t_reuse_artifacts_modules.html