"Using innodb engine" means that INNODB would be the default engine for creating tables, i.e. if you
CREATE TABLE a ... without specifying an engine for the table, it will be created according to the default engine.
If your tables are already created as MYISAM tables, it's meaningless to "use innodb". You are actually using MYISAM.
In other words - the DB has no engine, only tables have an engine...
See the manual here.
EDIT After question was edited.
YES - you should disable InnoDB.
Why? I assume this would save memory (but that's guessing).
From the manual, see the 2nd paragraph:
Turning Off InnoDB
Oracle recommends InnoDB as the preferred storage
engine for typical database applications, from single-user wikis and
blogs running on a local system, to high-end applications pushing the
limits of performance. In MySQL 5.5, InnoDB is the default storage
engine for new tables.
If you do not want to use InnoDB tables, start the server with the
--innodb=OFF or --skip-innodb option to disable the InnoDB storage engine. In this case, because the default storage engine is InnoDB,
the server will not start unless you also use --default-storage-engine
to set the default to some other engine.