How to get Postfix statistics of second instance?

By default, postqueue will give you information regarding your "primary" Postfix instance (where "primary" means "the instance using configuration files in the default location", which is generally /etc/postfix).

According to the man page, you can use the -c option to point postqueue at the configuration directory for your second instance.

Note that most of the postfix command line tools have a -c option.

Please take a look at the well-known pflogsumm script; it generates very complete statistics for each instance.

For postfix version 2.6 and later, you can use postmulti shipped by postfix. Excerpt from man 1 postmulti:

The postmulti(1) command allows a Postfix administrator to manage multiple Postfix instances on a single host.

postmulti(1) implements two fundamental modes of operation. In iterator mode, it executes the same command for multiple Postfix instances. In life-cycle management mode, it adds or deletes one instance, or changes the multi-instance status of one instance.

Thus for invoking postqueue of specific instance you can use postmulti -x, for example:

postmulti -i postfix-secondinstance -x postqueue -p