You will not be able to delete the decomissioned exchange servers when you have mailboxes in the exchangemailboxentry table pointing to that server. If these users are not exisiting anymore then you can just delete them from the exchangemailboxentry table. You should then be able to delete the server.
Regarding the archives this will depend on your business. You can delete these seperately if you do not care about these users data or just leave them and if you ever need to search them you would need to add a user manually to that archive VIA the VAC.