The performance is mainly related to the DBs.
Depending on the environment, sometimes, you have DBs located on different servers than the HTTP server.
The performance must be considered moreless like if you sum the total of hit on all the websites. The overhead of JMS is minor till 1,000 websites on the same server. Over 1,000 websites some specific setup might be necessary to speedup the processing.
If each website have their own DB that are located on different server, the performace is mainly related to the external server.
So the question is mainly related to the number of websites.
50 websites is very small.
We have few installation that have more than 1,000 websites and also one case with more than 10,000 websites.
You must better think in terms of what do you think if you put 50 standalones joomla on the same server with the traffic that you expect.
If you think that they can work without perfomance issue, this should be similar with a single Joomla and JMS.
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