It depends on how you add them to your document. If an image is linked it will have an X through it's bounding box when you select it, and a link icon in the corner. To embed it, click on that link icon and it will open the link menu (which is also located on the right of the screen) choose Embed.
The images you add to your Illustrator on the iPad document are embedded if you select them from the Image menu (photo icon on left tool bar) like from your camera roll or your libraries. If you choose a file from Creative Cloud (in that same image menu) there is a checkbox in the dialog popup on the left that lets you link it. Uncheck this and the file will be embedded.