Are there potential problems with per-subdomain installs?
I have done 1 CiviCRM per subdomain in a big project. About 20 separate subdomains with their own CiviCRM.

If settings are all correct then there is no side effect. They all just work.
With copying a CiviCRM to another Drupal instance (subdomain or not), you need to think about 


the connection between Drupal users and CiviCRM contacts
the CiviCRM table settings in settings.php
the user uploaded files, you probably want to copy all to 2nd CRM


Those subdomain Civis all handle their own SMTP. No issue there either. 

I don't know CiviSMTP, maybe you need an account per subdomain, maybe they can share the account.