Are we talking about the "flying night missions" bit - which is a historical fact (for example, here's an AA battery in Leningrad at night: https://commons.wikimedia.org/wiki/File:Anti_aircraft_Lening...) - or the "supply an encircled city with millions of inhabitants via a 30 mile boat trip across a lake straight into enemy territory" bit?
Man those goal posts move quick. The germans didn't try to shoot at small mobile targets on the ground/sea (i.e. not another airplane that has a giant sky behind it it stands in contrast from, because I'm pretty sure that's the next place these goal posts are moving) from the air at night. They didn't have the tech or the training fleshed out to make that effective, especially when the siege of Leningrad was taking place. End of story. There might be an exception or two but it generally wasn't done.
What you are proposing is nonsensical and not an effective use of resources, hence why they didn't do it.
It also didn't matter much because the soviets didn't do a ton of shipping over the lake by boat.