Here are all of the reasons I can think of against deleting objectively inferior duplicate posts.
—Dupes often have different commentary to the superior versions. For example, I often see Twitter compilations posted to Pixiv where the commentary is just "Here are my posts from Twitter over the last week/month!". Meanwhile, the commentary on each individual Twitter post is much more specific to the individual pieces of art.
—Favorites (and to a lesser extent, score) would need to be merged to the superior version. If I actually used favorites, I would be pretty annoyed if suddenly I have all these deleted posts in that list that I needed to go through and change over.
—Believe it or not, comments do actually have some value most of the time. Examples include (but aren't limited to) giving context to memes that the artist didn't give in the commentary and actual discussions on current events. Not every comment is a cringe-worthy roleplay about the pleasure of being cummed inside.
—It would require a massive effort to go back and delete the large number of dupes that already exist.
—Innocent users' upload limits could be destroyed. Additionally, it would artificially inflate some long-time uploaders' deletion counts, making them look like worse users than they really are.
—It might become less obvious which users are actually doing the work. Suddenly deleting duplicates could inspire a culture of 1-uppers who only copy tags from Twitter posts to their own superior Pixiv uploads, which in turn makes them look like a model user despite having put next to no effort into contributing to the site.
—For some artists, paid rewards would trump publicly released versions in terms of which is superior. I don't know about other users but to me making a paid reward the only active post seems like a shitty thing to do - that, however, might be another discussion entirely.
A less morally-rooted problem is the potential for a culture of piracy to rise up, where posting superior paid rewards whenever possible to nab the superior upload becomes the norm. This could have the same problem I talked about in my previous point, but may also result in a lot more banned artists due to Danbooru suddenly showcasing their paid rewards much more blatantly.
Now, despite all of these problems I'm actually in support of deleting inferior versions (except when it comes to paid rewards) - however, rather than deleting them perhaps a new post status should be created for inferior duplicates.
It would be similar to status:deleted or status:banned in that it would hide posts from search results, but different in that it would not affect a user's upload limit or increase their deleted posts count. Perhaps it could also avoid showing a green border on the superior post in searches, but still show any inferior versions when actually on the post page itself (this would still allow users to check for any commentary/comments that inferior posts may have).