Alec, For simple operations the performance shouldn't be a problem. One or two database hits isn't likely to be optimized. For a complex query, you can still have your session bean call the stored procs through JDBC.
If you call stored procedure by JDBC by your session beans. Does it means it is BMT cos you use JDBC (sql statments). So does it means that you must handle the low level transaction/rollback using getUserTransaction().