The decision about using separate databases was done before i got involved with OpenACS. Probably at that time the support for multiple schemata in oracle/pg was bad/not existing, so using different dbs for different instances was a no-brainer. The biggest advantage of the multiple schema approach is imho referential integrity across instances, which is not needed for OpenACS.
Separate dbs makes it easier to migrate/upgrade/save one instance, the security separation is easier, etc. but altogether the pros/cons are somewhat even (see e.g. )