Since the rust is localized, it would lead me to believe that there is (or was) a leak above the unit. Most of the rust from backventing that I’ve seen has been more evenly distributed - but anything’s possible.
5 (FIVE) elbows ??? That’s definitely too many elbows. I see an old mortared hole (in the chimney) right next to the water heater. They could have removed that mortar (seal) and used that side of the chimney. This installation will cause excessive condensation and rusting of the vent connectors.
Fuel burning water heaters shall be vented to the building exterior. The vent must extend from the top of the water heater at least five feet in length above the highest vent collar (CPC 517.2). The vent shall terminate at least one foot above a roof that is flat to a roof sloped 6/12 (CPC 517.3). If there is a horizontal section, that horizontal section’s length can only be 75% of the total height of the vent pipe (CPC 516.3) The horizontal section must have a continuous upwards slope of 1/4-inch/one foot (CPC 516.4).
As to the rusting at the top of the WH…I’ll bet if you place a flashlight on top of the rust spot (pointing straight up towards the ceiling), you’ll locate the source of leaking (past or present).