When ears are isolated it might be a usefull synergy effect to be able to host other applications on the same failsave cluster. But maybe its a bad idea to share an appserver-cluster for independend applications?
(maybe it leads to some kind of update hell?)
This is vendor-dependent. For instance, WebLogic Server has domains (a domain consists of one or more WebLogic Server instances and their associated resources that you manage with a single Administration Server). If two or more apps are in one domain, then you can't do things like change the service pack (to get for one app to work) without also forcing the other apps to run under the same SP.
Another thing to consider is that the parameter passing in EJBs is done by passing serialized copies of objects rather than copies of references. So, the callee cannot affect the objects of the caller.