You can use Photoshop's Image Processor to batch convert your Illustrator files into jpgs. (File/Scripts/Image Processor).
You can then relink to files with same name/different extensions via the links panel in InDesing (See below)
However, exporting InDesign docs as jpgs will not keep text or hyperlinks. They are flattened raster images when done.
Relink files with different file extensions
The Relink File Extension command lets you replace images based on file extensions. For example, if you have several JPEG images in your document, you can replace them with PSD files. The files with different extensions must be in the same folder as the linked files being replaced.
Make sure the files with different file extensions appear in the same folder as the original files.
Select one or more links in the Links panel.
Choose Relink File Extensions from the Links panel menu.
Specify the file extension to replace the selected files, and click Relink.