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Reporting my findings - might be useful to someone else.
In fact it seems impossible to reduce the connections used by arcgis server, or arcgis desktop for that matter.
Connections are always kept open with a transaction. So PgBouncer cannot optimize these connections. Why ESRI chooses to keep a transaction is unknown to me.
Also, arcgis server opens 2 connections to PgSQL for every mapservice. So if you have 20 mapservices you'll have 40 connections open in PgSQL. Only when a service is shutdown due to innactivity timeout do you get its connections closed.
This does not seem scalable at all to me. Maybe things will change in 10.2??