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I'd recommend this workflow if you want to use aperture, the import settings are powerful and you can have folders created for you automatically if you don't want to store images in the library.
NEF -> Aperture -> PSD if needed. Export JPGs as needed from aperture.
I've never run into an issue with aperture not showing a JPG, and it probably doesn't make sense to import this JPG to aperture for the reasons you state. For aperture to render PSDs, you need to have "maximize compatability" enabled as aperture will render the flattened psd.