This is possibly a color management issue. Edit: Color Settings. At the top does it say synchronized?
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I believe they may look, and print, quite different from the original RGB if placed in a CMYK Color Mode document.
You're right, it does appear to be a problem with the color mode. There is no change at all when I place a CMYK photo into a CMYK color mode document. However, as I frequently place grayscale images it is a problem because they become a touch darker. The change is enough that the details in the darkest levels get lost. Since all my work goes to a web press, all black and white art work must be grayscale. It can't be a CMYK build.
As long as your color management setup (calibrated monitor, settings, color profiles etc) is in working order, it is acceptable to place RGB images into a CMYK Illustrator document. You can also place grayscale images into a CMYK document and preserve the grayscale color space.
I would link, not embed the images.
For commercial print you can save a PDF from Illustrator. With the proper settings the RGB content will be converted to CMYK when you save the PDF. You do not need to embed the images prior to saving the PDF, linked images will be included in the PDF output.
You want to be sure that the Illustrator Document CMYK profile is appropriate for the print condition you are using.
In Photoshop, to see the same color in the RGB image that you see in the Illustrator CMYK document, use View: Proof Setup and Proof Colors. Then you can see the on-screen CMYK rendering of the RGB image.
RGB images can definite take a hit when moving to CMYK. That is just the nature of CMYK.
However, as I frequently place grayscale images it is a problem because they become a touch darker. The change is enough that the details in the darkest levels get lost. Since all my work goes to a web press, all black and white art work must be grayscale. It can't be a CMYK build.
Illustrator does not have grayscale color management. All gray images display as K channel according to the document CMYK profile. So the grayscale images will not appear the same as they do in Photoshop.
To see the same thing in Photoshop, duplicate the image. Delete everything in the duplicate. Mode CMYK. Go back to the grayscale image. Copy the gray channel. Paste this into the black channel of the blank CMYK document.
In Illustrator you can see that the grayscale image is indeed black only. Use Window: Separations Preview in AI CS4. If you don't have CS4, you can always check a PDF using Adobe Acrobat with Output Preview, to see the ink separations there.
I do not have this issue with placed photos in InDesign, only Illustrator. Very confusing!
This is because AI only supports one color mode per document (RGB or CMYK). InDesign supports 3 - RGB, CMYK, and DeviceN.