You have been doing a great job documenting that team, Ben! The category now contains more profiles than any of the Major League Baseball Teams categories. It does not need to be a personal category -- it is fully qualified to be a real category.
I added the category to Category: Sioux City, Iowa because this team clearly is part of Sioux City history, regardless of its position within Category: Baseball. And I took the liberty of submitting a "Rename Category" request for the personal category, to change it into a regular category. I expect that the Categorization Project will review the situation and ask EditBot to finish the process of converting it into a regular category.
I cannot explain why Category: Minor League Baseball Teams was deleted, but I can guess that it was created as a completely empty category and was deleted for lack of content. It is also possible that there was some discussion of whether "Minor League Baseball Teams" was the appropriate name for the category. There is one other minor league team with a small category listed at the top level of Category:Baseball, so the Sioux City Soos would have company in "Minor League Baseball Teams."