/opt directory is a good location for the program distribution files. The
/srv directory is used for the programs run-time data. (Please see the Filesystem Hierarchy Standard.) Unlike the
/etc directory where the standard indicates that the
/opt/<pkg> configuration files should be placed in
/etc/opt/<pkg>, there is no standardization that
/srv/opt/<pkg> should be a parallel structure (although it's probably not a bad idea).
/opt/webserver/ (your node.js application)
config.json (configuration file for your web server)
/srv/opt/webserver/ (opt subdirectory suggested, but not required)
Please keep in mind that this is the general case, and is not unique to express applicaitons.
Hope that helps,