What will happen if I restore backup DB with empty session table? It seems that only the session is really big compared with other tables.
Is there any bad effect to Drupal site if I restore my backup Mysql file after deleting all the rows in session table?
The main issue is that people will need to log in again.

A side effect of this is that any session data that your site may have saved for users will also be gone.  This is usually a nuisance, and not a major problem, though.

Personally, I have never had any problems caused by either not restoring {sessions} or manually clearing out the table, either via DELETE FROM {sessions} or a drush command.