For a project we having a bunch of data that always have the same structure and is not linked together. There are two approaches to save the data:
I don't know mysql very well, but I think I'll have to give the standard performance answer -- "It depends".
Some thoughts (dealing only with performance/maintenance, not database design):
However, to contrast, having multiple databases means the server will probably be using more memory (since it has multiple caches). I'm sure there are more "cons" for the multi-database approach, but I am drawing a blank now.
So I suppose I would recommend the multi-database approach. Obviously this is only with the understanding that there may very well be a better "database-designy" way of handling whatever you are actually doing.