IMHO the main difference between those two cases, regarding performance, is the database size. If you have 2 really huge sites. Huge means like half of a million of objects with lots of attributes. Having 2 of sites like this in one database is very demanding for db.
Even in that case you don't need to have 2 instances, just 2 databases with 2 var storage folders.
ok! currently we already have two separated databases and two var directories but i would know if we can have better performances if we choose to separate the two sites on two differents instances.