Say, LazyWizard. Could you maybe merge messages? Have a single message that says something like "Omnifactory inventory update: blah_laser (12/20), some_missile_thing (4/10), ...", etc?
Not 100% sure how the message display deals with line-wrapping, so there might still need to be some cleverness to deal with that, but it'd help cut down on the spamminess of the mod's messages, without actually cutting out information.
Maybe even add a mid level of output, where it just says "Omnifactory constructed new weapons" or the like?
It might also be neat if you could specify supplies or fuel per weapon / ship constructed, rather than per day. Though that might get unreasonably clunky / unintuitive in terms of what order things get constructed in when there aren't enough supplies to build everything at once, so it may not be worth the trouble.