I think it is correct, I have mix storage engines in a databases, and the speed of database is right.
Anyway if you uses opencart with a lot products (50,000), I recomending you that you created index on (all) of your tables, if you do that you can improving your speed.
I did the following:
#Tabla category campo parent_id
CREATE INDEX i_parent_id ON category (parent_id);
#Tabla category_description campo language_id
CREATE INDEX i_category_description ON category_description (language_id);
#Tabla category_path campos path_id y level
CREATE INDEX i_category_path ON category_path (path_id,level);
#Tabla category_to_store campo store_id
CREATE INDEX i_category_to_store ON category_to_store (store_id);
#Tabla manufacturer_to_store campo store_id
CREATE INDEX i_manufacturer_to_store ON manufacturer_to_store (store_id);
#Tabla product campos manufacturer_id, date_added, date_modified
CREATE INDEX i_product ON product (manufacturer_id, date_added, date_modified);
#Tabla product campos model, sku, upc, ean,(como veis donde tengais la referencia etc) y con tipo FULLTEXT (si el campo es de caracteres no de números)
CREATE FULLTEXT INDEX i_product_fulltext ON product (model, sku, upc, ean);
#Tabla product_description campo language_id
CREATE INDEX i_product_description ON product_description (language_id);
#Tabla product_to_category campo category_id
CREATE INDEX i_product_to_category ON product_to_category (category_id);
#Tabla product_to_store campo store_id
CREATE INDEX i_product_to_store ON product_to_store (store_id);
#Tabla setting campo store_id, serialized
CREATE INDEX i_setting ON setting (store_id, serialized);
#Tabla url_alias campo query con tipo FULLTEXT
CREATE FULLTEXT INDEX i_url_alias ON url_alias (query);# 6936 filas afectadas.
#Tabla zone campo country_id
CREATE INDEX i_zone ON zone (country_id);
#Tabla zone campo name y code con tipo FULLTEXT
CREATE FULLTEXT INDEX i_zone_fulltext ON zone (name,code);
You will have to put the 'prefix' on your tables.
Something like this:
http://www.codigojavaoracle.com/desarrollo-web/mejorar-la-velocidad-en-opencart/