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I can't think of any reason that performance would suffer on mysql, and even if it did, it would only be noticeable on a huge site or overloaded db. The only drawback I can imagine is that if eventually one of your applications grows a lot and you need to move it to a separate server, you'd then have to separate the dbs, but in mysql that would also be pretty easy.
Now really this isn't a huge thing but if you are allowing personel from site X to write queries themselves then they will have access to the tables of site Y, they would be able to query them and delete/update data.
If you are the only one writing and executing SQL then you should be fine.