Yes, this is an issue we already have good data on. In our testing even just closing the inspector tab can improve performance, rather than fully converting to an inline workflow.
Along those lines, try disabling the Open comments in inspector option (which applies to footnotes too) in the Editing: Options tab of File ▸ Options.... This will prefer using a pop-up for viewing and editing notes, so long as the inspector is not already viewing the Footnotes & Comments tab.
I’ve never seen dramatic performance issues with inline annotations or footnotes (way more annotations for me, but that really shouldn’t make a difference as they are virtually identical in terms of tech), so I’m not sure if everything is exactly the same. Are there any other conditions that might stress the text engine, like using a more “expensive” view mode like Page View, Scrivenings editing mode, line numbering, or even just having lots of images in the editor?