I figured it out now, on the 1st page of this thread, the first "MP5" download link is an old version "v1.1", while the armaholic link is newer "v1.25" The old version is not compatible with something and caused the issue.
When I activate your latest version of the MP5 Pack, the vanilla 9mm suppressor is gone, along with the ones included in your pack. Zero other mods installed, just HLC core and the MP5 Pack.