Stoppers do turn up, honest - they're often listed on their own on ebay.
I think it was fairly arbitrary whether they had stoppers or not. They're not made to fit exactly, they have a long "tail" bit, a lot narrower than most inside necks.
In the early days, a lot of Mdina was exported to Germany - it's not necessarily "well-travelled".
This particular ink pot has Mdina in Michael Harris' hand on the polished round pontil mark too!