The way they knew they were women is they captured them or read Soviet propaganda.

There's a book that came out in 1994 called A Dance With Death by Anne Noggle. According to Goodreads it looks like there's a kindle version. I got it though ILL.

The book is comprised interviews with former Night Witches. They talk about what their service was like. The pilots are all very upfront that their planes were cheaply made and very vulnerable. The way they conducted a raid was to climb high then cut their engines so they didn't make sound. Then glide in over their target and drop their bombs then crank their engines as the pulled out of their dive and turned back to their own lines. They did this b/c they just had canvass and wood framed planes for the most part and they had to delay discovery as long as they could to avoid anti aircraft fire. They were flying old Polikarpov U-2 biplanes that had been used for training. There's lots of pics on the internet so you can get a sense of how flimsy the planes are.

So if a pilot was at the tail end of a raid, there was a decent chance of they'd be spotted and from there it wasn't much to shoot them down. And if they crashed too close to the German lines it wasn't hard to piece together that the injured woman with the flight gear on (These are open cockpit planes flying in night, often in the winter) near the crashed plane was probably the pilot.

On top of that, the planes didn't have the longest range, maybe 250 miles/400 kilometers. So they're hitting targets a max of 125 miles from their landing strip or staging area. The Noggle book is just from the knowledge of the pilots she interviews, but we can pretty safely assume that there was some German scouting and spying of their landing fields where they saw who the pilots were.

Also, the Soviets weren't quiet about their success. They published stories and propagandized the accomplishments of famous women pilots like Yekaterina Budanova and Lydia Litvyak. Although they weren't Night Witches, a few of the interviewees mention their admiration for them as being the inspiration for joining the Night Witches. So the idea of female pilots in the Soviet forces wasn't a secret or something the Germans would have been unaware of.

The interviews are interesting. The pace of their missions were so hectic. And b/c the nights in the winter are long, they were sometimes flying 3 missions a night. There are a few interviews where the pilots talk about regularly taking speed and difficulties readjusting to a normal sleeping schedule after the war. I found the number of missions these women flew, since the war started so early on that front, and how young the women were mindboggling. I think the US pilot in the ETO with the most missions had 500ish. If you figure 180 days of winter flying 3 missions a night, if a pilot lived, she would have had that many by the spring of 1943. I was also surprised to learn about the number of women's flying clubs before the war which created a pool of women that could be put into this type of service.

The book obviously has the problems all books that rely on oral history due, but the interviews were taken at a time when strict Soviet message discipline had long since evaporated and there's enough interviews, broken up into small sections addressing one or two topics at a time, that you can get a sense of their reliability based on how in line they are with the other interviews.

I would recommend it if you're curious about the Night Witches at all.

https://www.goodreads.com/book/show/1624103.A_Dance_with_Death