A couple of things to consider:
*) MySQL provides FULLTEXT indexes but only on single tables (i.e. it won't mix more than one table in an index).
*) You can, of course, use a SELECT statement collecting fields from mutiple tables and use WHERE filtering on those fields. But do you want to use OR logic for each field or AND logic?
*) I hope I'm not being rude, but are you sure you actually need lots of tables, or would you be better off with lots of rows and one table?
*) If your data is not tabularly structured, should you consider an document-centric approach using, for example, XML?