Is there any performance hit from querying over two (or more) databases on the same MySQL server, compared to if those databases had been merged into one?
Background
This would only introduce a noticeable problem if you were trying to use multiple select statements for the data in each database. It would be better to use some foreign keys, and then use a single join query to get a user's data and his associated user content. You can prefix schema names on your tables in the select join statement.
example would be similar to this:
SELECT a.user, b.user_content
FROM database1.table1 AS a
LEFT JOIN database2.table2 AS b
ON a.user = b.user_id;
No. In MySQL, "databases" are essentially just catalogues which have no effect on the way data are stored or queried.
Querying two tables in different databases is the same as querying two tables in the same db, from a query execution standpoint.