For a number of reasons, AI (Adobe Illustrator format) is the preferred file format instead of EPS for placing Illustrator artwork in InDesign. However, there is one small drawback to the AI format. If you have an AI file that contains only black or spot colors, and you place the AI file in InDesign, the Preflight command (File > Preflight) gives a false report. In the Colors and Inks section of the Preflight report, process C, M and Y will be listed as being used, even if they are not used in the AI file.
This is unfortunate, since in this case Preflight is no longer helpful as a way to see if you mistakenly used process colors in your layout. The best workaround is to choose Window > Output > Separations Preview, and examine the C, M, and Y separations individually to make certain that no objects using these colors appear on your pages.