Remove stock android apps via file manager
Assuming your HTC One is running Sense, it sounds like your phone is S-ON (locked). Naturally, with S-ON, any change you make to the system will be undone on the next reboot.

I'm not sure if there's a working S-OFF (unlock) method available for your device, as a quick Google search turned up varied results for S-OFF methods on the M8. Take a look at SunShine S-OFF, if you want.

If you don't want to go that way or if your phone's already S-OFF, you may want to try Titanium Backup's "Bloatware Melter" feature (TB menu > Preferences... > Bloatware Melter) specifically made for NAND-locked devices.

You can also try to delete the app files themselves inside /system/app and/or /system/priv-app, like you said; but do be careful if you do this - you might accidentally delete something else.