..."We have the fonts we need, but need more sophisticated control over kerning, justification, auto-flowing of type, etc."
- Everything built in the suite is meant to complement eachother. Illustrator has the same robust typography tools as InDesign, with ID having a slight advantage with Style Sheets.
..."Links - hundreds of our artworks will need to link to the same brand logo, which is currently vector."
- In Illustrator, the logo is part of the file and does not need to be linked. Other items such as UPC Codes, image files are linked upon "Place".
You might consider some type of export out of ID into Ai. Something like Save Page As > EPS, then open the page file in Illustrator.