The server runs php 5.5.38 with apache2.4 and MySQL 5.5.62 there are about 5k-10k read write per minute.
And the table of main use was MyISAM and started crashing, saying "in use" instead of stats. The attempts of repair failed. And finally changed it to InnoDB and stopped but what can I do to prevent the errors?
MyISAM is obsolete technology. InnoDB is ACID compliant and designed for crash recovery. This is the solution.
For example, the default engine in MySQL 8.0 is InnoDB: https://dev.mysql.com/doc/refman/8.0/en/storage-engine-setting.html
You should also implement some caching at the PHP level with Redis/Memcached/Files to prevent unnecessary reads.
Make sure that you have indexes on the columns used in join/where clauses.
https://dev.mysql.com/doc/refman/8.0/en/mysql-indexes.html