Optimizing a query on Mysql 5.5.24
Without some way of tying the two tables together, you are asking for 6 million rows (6000*1000).

Instead of FROM employee e, employee_categories ec, you need something like

FROM employee e
JOIN employee_categories ec  ON e.category = ec.category


AND... be sure category (or whatever it is called) is indexed (perhaps PRIMARY KEY) in one of the tables.

Those changes should speed it up by a factor of 1000 or so.

The Query cache is irrelevant (and generally should be turned off).