I am not sure if I have resolved the issue, but I managed to delete my duplicates fairly easily by sorting them by date added and selecting all the ones that were created during a certain sync. I then sort by name or duration and pick out those that aren't duplicates. Still tedious but better than brute force

If you look in the iPhone user manual - in the section on Voice Memos (Chapter 28, page 105) - it walks you through the intended process for syncing with your computer.

http://manuals.info.apple.com/en_US/iphone_user_guide.pdf

Sharing voice memos with your computer

You can sync voice memos with the primary iTunes library on your computer, then listen to memos on your computer or sync them with another iPhone or iPod touch.

When you delete a synced memo from iTunes, it stays on the device where it was recorded, but is deleted from any other iPhone or iPod touch you synced. If you delete a synced memo on iPhone, it's copied back to iPhone the next time you sync with iTunes, but you can’t sync that copy back to iTunes a second time.

Sync voice memos with iTunes: Connect iPhone to your computer, then in iTunes select iPhone. Select Music at the top of the screen (between Apps and Movies), select Sync Music, select “Include voice memos,” and click Apply.

Voice memos synced from iPhone to your computer appear in the Music list and in the Voice Memos playlist in iTunes. Memos synced from your computer appear in the Voice Memos app on iPhone, but not in the Music app

iTunes should actually sync Voice Memos if you have the option 'Sync Voice Memos' checked in the 'Music' tab when the iOS device is connected (either through USB or Wifi).

I actually forgot I had this item checked in iTunes, and noticed I had a new playlist named 'Voice Memos' in iTunes. These were rather short (only a minute to 5 long I think), but synced ok.

If you delete a Voice Memo from the iTunes Library, it will not be deleted from the device on which it was recorded, as stated by the Manual, the next time that device is synced. In fact when you re-sync that device again, it is possible to have that Memo (which had been deleted from the iTunes Library on the computer) be copied back again into the iTunes Library on the computer, by checking the Include Voice Memos on the Device/Settings/Music page (as of iTunes 12.11.0.26).

Additionally, if the iTunes Library on the computer is empty at the time you connect a device on which some memos have been recorded, these memos will not be erased on the device when you sync; on the contrary, they will be copied back to the iTunes Library on the computer, no matter if Include Voice Memos is checked or not on the Device/Settings/Music page. Do not be deterred by the warning message in iTunes :

This iTunes library is empty. If you link the iPhone [device name] to this library, all songs on the iPhone will be erased. Are you sure you want to continue?

as this will not apply to the Voice Memos which were recorded on the device (as of iTunes 12.11.0.26).