I did some further digging and cleaning of directories on my system.
I discovered remnants of a JACK server install on my system (
http://www.jackosx.com/). This didn't seem to be an issue with earlier versions of OSX and/or Reaper, but cleaning the directory and rebooting seems to have resolved the issue.
For posterity, the directories in question were located under /Library/Audio/Plug-Ins/VST and /Library/Audio/Plug-Ins/Components.
Reaper is now booting in 2-3 seconds.