The site is a little bit slow because of installed heavy zencart application
What's the meaning of heavy in the above sentence? Does it mean the application is too large or something else?
In this context, heavy means 'using a lot of resources' or 'placing a (heavy) load on the computer running the application'.
A single word replacement might be difficult to find: heavy is quite descriptive.
Pavium's answer is, of course, absolutely correct, but I want to expand a bit.
You asked "Does it mean the application is too large?" The answer is no. The application takes up a lot of resources, but that may be necessary because of the nature of the problem the application is solving. Describing an application as heavy neither implies or denies that the application is too large -- it just says that it's large.
If one wanted to say the application is "too large" they might say it is "inefficient" or "poorly implemented."
I would also add that describing software as "heavy" is uncommon. One would usually either say "heavyweight" or probably just "not lightweight."