Hi Julie,
Sorry for the delay on our part.
The short answer is just "legacy", really. The reason JHOVE was originally chosen (and, as Phil said, we've been using it "forever") was that we needed something to help identify the mime types of uploaded files, and that was a) something readily available then and b) another Harvard-developed and maintained package. The latter part hasn't been the case for a longest time (but at least it appears to be actively maintained now, after a long hiatus, by the Open Preservation Foundation). It is entirely possible that there are better software packages available by now. We just haven't gotten around to evaluate any alternatives, because, "legacy".
I should mention that Dataverse does not solely rely on JHOVE to determine the mime type of an uploaded file. There are several ways of detecting, or guessing the content type, and then Dataverse will make an educated guess as to which type to use. For example, we have our own code for identifying the formats that we recognize and support for producing data- and variable-level metadata - such as Stata and SPSS. If one of these tests produces a positive result, the type produced (for example, "application/x-stata-14") always wins over whatever JHOVE says. Dataverse will also check the type that the browser or the API client supply with the upload. There are situation where that will be the "richest"/most specific mime type available, and therefore chosen over the JHOVE-produced result. There is also the "direct upload" workflow, where the file is uploaded directly to S3/Globus volume, bypassing Dataverse. This is much more efficient that streaming the data through Dataverse and much better suited for large uploads. However, the drawback is that Dataverse cannot perform any content type detection during the initial upload workflow, via JHOVE or otherwise, since it never sees the actual data bytes. So it has to rely solely on the type supplied by the browser, or on guessing the type from the filename extension (Dataverse maintains the list of extensions for this purpose).
Hope this helps.
Best,
-Leo