E-Boats when they had an Enigma, used the M3. The most common radio net for the surface fleet (including E-Boats) was NEPTUN. Many boats did not not have an Enigma and instead used the RHV coding system. RHV stands for Reservehandverfahren. I'm generating the 25 bigram tables you would need to do the RHV. Those "might" get published by 1 January, but not sure there. I have a Quick Reference Guide written.
B123/AAA no stecker AAA ABC 1tle 1tle MHLS AYUW LFCE RQCY ESLI ERSD RDAL YCQY EJ
A former e-boat commander said that in Norway all boats had an Enigma. Only when the boats were used in the canal did the Enigma´s disappear and it was encrypted by hand. So that would fit. But it wouldn't have to be the Niboe key.