No, there's not a separate system for Europe as the American Iris Society is the official world registry for rhizomatous irises.
There is a separate system for bulbous irises (Dutch, Reticulated, etc.). The official world registry for those is the Koninklijke Algemeene Vereeniging voor Bloembollencultuur (KAVB)
https://www.kavb.nl/, based in the Netherlands. KAVB is also the official registry for tulips, Dutch hyacinths, and many other types of plants that grow from bulbs.
Many of the duplicate entries in the Iris Database are a result of the fact that there are two different registries handling the rhizomatous and bulbous irises. I've thought about asking Dave to split the bulbous irises into their own database, but it might create more problems than it solves.
There are a few different reasons why you might receive unregistered irises from a commercial grower:
1. The big one is that publication of the AIS registry can lag more than a year. For example, if a hybridizer registered a plant in January 2017 and made it available for sale this spring/summer, you could potentially see it blooming in you garden before AIS publishes its registration information, which will occur around late April 2018.
2. Some hybridizers introduce plants, but don't register them until a later time.
3. Some growers don't register their plants at all.
This last reason, in particular, creates all sorts of confusion and it's why we are rather reluctant to add unregistered irises to the database without a fair bit of background information.
As for 'Hermes', it IS possible re-use the name of a previously registered iris. I believe it can only be done if the original iris is no longer in existence, doesn't show up in the parentage of any other registered iris, and I think you need the original hybridizer to release the name (not sure what you do if that person is deceased). There are probably other hurdles I'm unaware of as well, but it can be done.