Ideally, DKIM-keys should be rotated regularly. Besides that cryptoanalytic progress could make it necessary to upgrade key lengths or algorithms.  
As SmarterMail generates DKIM keys for each domain individually, rotating DKIM-keys is fairly time consuming to achieve for a larger setup.  

I do understand that having different DKIM keys may have a security benefit.
If domains were heavily sandboxed it could be better to have only a single domain's key compromised. To my understanding however, the 'settings.json' files in which the DKIM private keys are stored, are readable by any Windows user; so the sandboxing argument does not apply.  

Another argument might be a prevention against header spoofing by other domains on the server.  

The ideal solution would be, in my opinion, to have a single DKIM key per server; for example:

→ hostname._domainkey.example.com TXT "v=DKIM1 [...]"

All domains could have their DKIM records pointing to the server DKIM record through CNAMEs; for example:

→ 3bde06e4._domainkey.otherexample.com CNAME hostname._domainkey.example.com.

Giving all the domains different DKIM selectors would prevent the spoofing of the From-header by other domains on the same server, but would allow for very quick key rotation.  

Having a single server-wide DKIM key would speed up significantly:
→ regular DKIM key rotation,
→ key length or algorithm improvements,
→ incident based key rotation (which must be quick!)