When I set up my RT, i didn’t have a (sub) domain name so I just left it
to our domain name. Now I got the domain name and would like to change
the text in the subject [domain.name #no] to reflect this, but in
RT_SiteConfig.pm it states:

Your domain name is recommended, so as not to pollute the namespace.

once you start using a given tag, you should probably never change it.

So can I change that or is that $Organization parameter that shows up in
mail subject?