Sorry for bumping an old thread, but I have the same problem (or a very similar one) - unwanted conversion of transparent grayscale images to DeviceN, when exporting to PDF/X from Indesign. It can be PDF/X-3, 4, it doesn't seem to matter.
In my case, the problem affects only the transparent images, but also the the non-transparent images located on the same page with them. The rest of the content exports correctly.
The export settings are set to NO CONVERSION, but Indesign makes a conversion anyway. The transparency blend space in Indesign is set to CMYK.
The images are just grayscale, they use no other color except K. I've never assigned any other color to them, I never wanted duotone or something.
But Indesign is converting them to this DeviceN nonsense and they should be DeviceGray.
Acrobat's Object Inspector identifies this as: DeviceN, colorspace: Black, while Pitstop Inspector says: 1 spot color (monotone).
Basically, Indesign converts your hard work to something unwanted and you have no control over it. Some users might not even notice this, especially if you have lots of images.
Thanks