If you want to use a linked Illustrator file (a logo, for example):
- save it as a .ai file (if you want to be able to click on it to open it in Illustrator)
- keep it it the Links folder with placed images
- it will be directly integrated into the final SVG, not linked to
Note that when placing a .ai file, Illustrator uses the saved PDF information and not the Illustrator source. This means that it must be saved with “Create PDF Compatible File” checked.