Three years ago a discussion was launched on the Pgbouncer mailing-list  about the JDBC Driver which does not disable prepared statements when using
?prepareThreshold=0 in the connection string.
At Clever Cloud, we provide PostgreSQL databases behind PgBouncer to handle pools of connections. And to optimize these pools, we use the transaction pooling mode. This mode will prevent clients from using prepared statements as the session is only used for one transaction.
To be able to use this mode internally we manually applied a patch to the driver. After 8 months of inactivity, the pull-request  was finally merged into the master branch of the driver.
Now we hope that the next version will be released soon.