As I see it, there are several use cases for IIIF objects in Omeka.
For purposes of preservation and stability, many faculty, scholars, and project leaders may be interested in using Archive.org to host previously unpublished materials. If you go “archive first”, rather than “archive as a backup”, then all of your materials / collection are in Archive.org, but lost in a sea of other things (sure you can make a collection page too).
In this case, let’s say you wanted to create a search and discovery interface for this collection, which has been published to Archive.org - then, the IIIF import with both metadata + images is desirable. Of course, you’d probably want to then add additional metadata to the objects in Omeka-S, which is not part of the manifest.
2nd scenario, if you are publishing your “primary” digital objects within your Omeka installation, perhaps you will have a spreadsheet with metadata about each object, which is easily imported and can include a IIIF manifest link, which then allows viewing of the document in Mirador or UniversalViewer. You still get the benefit of scenario #1, and you don’t have to take up (potentially lots of) hard drive space locally.
3rd scenario is that you fully publish metadata + images in Omeka, but have an “alternate version” pointed to Archive.org. In this case, you could also install the IIIF Image Server module and display the images with a document viewer + serve the Omeka-based IIIF object out to the public - but if you are working with high resolution images or very large files, it may be desirable to let Archive.org handle the IIIF functionality.
Particularly when dealing with unpublished scholarly collections which are not part of the library repository, aka many digital humanities projects, I think an Archive.org-first solution is best, with an understanding that the Omeka-S site may have a lifespan of ~5 years as opposed to 10+ unless there is funding to maintain it.
Overall, academic / university IT are becoming much stricter about security and maintenance, unlike prior generations of instances, installations, and custom web apps that could sit on servers for 10+ years without updates.