Also, can you add a unit test?

I think the unit test should be in aedes-stats project.
I will add the code
doPub('version', aedesInstance.constructor.version)
in aedes-stats iterate() function https://github.com/mcollina/aedes-stats/blob/master/stats.js#L52

Add to prototype could be, but it will require an extra memory for storing version in each instance, and it is not useful for user except aedes-stats.
Version won’t change in each instance, except a user packs two aedes package. In this case he still can get different version using aedes.constructor.version, right?

My idea is also be memory-wise

The following will not cause any addition memory allocation:

Aedes.prototype.version =  require('./package').version

The reason for that is that it will stick the value on the prototype itself. Instances will look the value there, much like any additional function.