Yes, MySQL extension works only with MySQL 4.x or later.
If you need to work with older MySQL version then you can manually create generic driver using Driver Manager (I believe you may use the same jar library which is in $USER_HOME/.dbeaver/drivers/mysql/ folder).
Unfortunatelly you won't be able to work with custom MySQL types, procedures and other features provided by MySQL extension. From the other hand MySQL 3.x doesn't supports procedures and most of other modern features
Hope it will help.