We're using full SQL replication and as far as I know, the document numbering schemes are having no issues with being used across multi-sites so on face value, I can't see why the Item numbering schemes should.
Technically speaking again, I get the 'if a workgroup goes down' theory but to be honest if a business is large enough to justify having multi-site replication, it'll be sitting on a pretty good IT infrastructure so although you can never say never, it's a rare occurence for a site to compeletely go down. However, item's being created is an event that occurs multiple times, hundreds of times per day.
In addition to that, I worked in the reseller channel for nearly a decade and this was never publicised by Autodesk, I had no idea that we needed to consider this when building multi-site implementations. A Google search for "autodesk vault item number replication" returns zero information on this and confirms that I haven't missed an technical publications on this story.
The concept of having a numbering scheme per site isn't a practical one, if you allowed the option of defaulting a specific numbering scheme to a specific site then it would be close to being a considerable option. If it was up to me, I'd consider altering product behaviour to either:
1) Provide an administrative option whereby if a workgroup goes down, prevent any Items being generated. Then it's up to me, if a site goes down I can simply stop Items being made until things come back online.
2) Keep the current existing workflow, but in the event of a disconnection between publisher and subscriber, when the failed site comes back online, Vault creates an ADMS task to automatically renumber any Items created during that time with the [@WORKGROUP suffix], giving them the next available number. Warn all users with an in-client prompt that the Items they're creating may be automatically renumered when the system fault is resolved.
3) Most if not all everyday Vault users are not going to have a clue about what we're talking about here, so when this numbering conflict occurs through standard workflow, at least give them an in-client prompt or warning explaining why their Item number isn't now what they first thought it was.
4) Make the Item numbering schemes work the same way as the document numbering schemes!
I can think of many more options, most of which including the above are all much more favorable than what we have now which is Vault modifying production data at will without any warning to the user.