Actually, InDesign doesn't place Illustrator files; it places PDF files. Thus, the only .AI files that can be successfully placed into InDesign if the following three are true based on the options specified when first saving the Illustrator file:
(1) The Version specified is Illustrator 10 or newer.
(2) The Create PDF Compatible File option is selected.
(3) The option for including ICC profiles is selected.
Otherwise, the .AI cannot be placed successfully into an InDesign document! Although the third consideration above doesn't affect whether the .AI file can be placed into an InDesign document, if the ICC profiles are not in the PDF-compatible .AI file, not only are the ICC profiles missing, but the objects are specified as DeviceCMYK or DeviceRGB, very likely resulting in color anomalies in your InDesign document for the placed content and resulting final output.
Furthermore, since it is possible to open such PDF-compatible .AI files in Acrobat or other PDF file manipulation products, it is possible that the PDF portion may be modified without modifying the source Illustrator content. In other words, it is possible that you lose synchronization between the Illustrator content versus the PDF content, noting that what gets placed in InDesign is the PDF content, not the Illustrator source content which is stored in the PDF file as private data (PieceInfo).
Another issue to be aware of is that when saving PDF-compatible .AI files, raster imagery is saved as if when explicitly saving PDF, the image settings are for ZIP-compressed, non-downsampled images. This is non-lossy, but could result in unnecessarily large files.
That having been said, I most strongly recommend that Illustrator files not be placed into InDesign. Rather, a more reliable workflow practice is to use the Save as Copy and select PDF. For the options, choose the Adobe Preset labelled PDF/X-4:2008 which actually uses the PDF/X-4:2010 standard. You may modify the detailed settings to meet your needs (especially image downsampling and format), but as-is, they will normally provided very high quality graphics. Place the resultant PDF file into your InDesign document!
- Dov
Updated on July 19, 2019