Get a copy of Acrobat Pro to check your output files. You can open your AI file n it as long as it has been saved with PDF compatibility (which is the case since you can place it in InDesign).
I usually use pdf color separations from illustrator to check colors. Last week I upgraded OS and I had a problem with illustrator, when I tried to stamp the logo, the system crashed, so I used indesign to check colors. Now I solve the problem and I check the colors of logo whith pdf, also the shadows are pantone.
Many thanks.