Hi, there are a few questions in your post so let me try and answer them:
I presume AP3 is best used in the 'Managed files' way, right?
Not necessarily. It makes backing up easier but it's also less flexible than a referenced library. Both are perfectly good choices and depend on your situation. Look up referenced vs managed in this forum for a slew of great answers.
the ones I got in the DxO library, or these in the iPhoto.
If you sent JPEGs to iPhoto and then modified those, I'd tend to go back to the DXO versions and treat those as masters (you don't want second or third generation lossy originals). If on the other hand you sent TIFFs to iPhoto then you could import that library into Aperture - you'll get both originals and modified versions in the import.
I cannot stick always to RAW only, because JPEG's still remain important to design photo books by some
RAW can never be used for anything other than processing and will always need to be exported or rendered to another "distribution" format. So Aperture doesn't change anything to this other than the ability to create certain things natively (books, slideshows) without first having to export those files.
Is there some particular workflow I have to respect concerning Aperture, since the proper working of DxO's 'optical modules' system and optical corrections on my Nikon D80 (Nikkor zoom 18-200 mm) needs to make use of DxO first, then Aperture?
To be honest, using another RAW decoder is going to complicate your life immensely. I really think you should try Aperture 3's RAW decoding and see if it works for you. Check out the decoding options, see if the default works. If it doesn't try tweaking the settings. If you find a setup that works you can save it as a preset and apply it automatically on import.
The advantages to only working in Aperture are immense. It means you can keep your entire workflow RAW and/or non-destructive most of the times (unless you use plugins or external editors) and it simplifies organization.
If you absolutely want to stick with DXO - and since Aperture can't use an external RAW decoder (no other DAM does either for that matter) - you'll have to:
1. Import your pics in DXO.
2. Decode and apply adjustments.
3. Export to a folder on your hard drive.
4. Import those processed pics into Aperture.
This means you'll be duplicating all your pictures. And ideally you'll be exporting TIFFs, which means much larger files than your original RAWs.
Frankly I'm not sure I see the point of working like this unless there is a magnitude of difference in RAW rendering and image processing with DXO. It's a recipe for a huge headache and a lot of time wasted IMHO.
But only you can be the ultimate judge of that….