Is Hibernate less effective in some environments, like a polygot company where several distributed systems are accessing the same db? If Acme Company has a python website reading from and writing to the same database as a java web app (web services), will Hibernate be a poor choice for the java web services app? In other words, does Hibernate caching and session management assume all db transactions for Acme will be using Hibernate? Do I need to be sensitive to certain ORM concerns at a company where several programming languages are writing a lot of updates to the same data concurrently? Is Hibernate more advantageous for a strict java shop using a java ee app server for nearly all of its business operations?
Hibernate does have some performance overhead over pure JDBC, but if you're using it cautiously it should be fine for most of use cases.
Hibernate does not assume that it handles all operations itself. The only thing I would worry about is second level cache if you need it. You won't have a way to keep it in sync if other apps access the same DB (but you don't have to use it).
Having said that, I must add that having multiple apps write to the same DB is not a good practice. I'd rather create one app that handles this DB and have others communicate with this one - this way it's much easier to keep the database consistent.