Hi Zezicla,
If you truly have 1000 players, with a lot of data in MySQL; InnoDB is what you should be using.
MyISAM is quicker when you have less SQL data, however, if your database exceeds GB; then you'll see that queries begin to lock up from time to time... causing lag. That is where InnoDB outperforms MyISAM, when your SQL database is extremely large; it does not lock up.