I was doing a bit of crew customisation when I noticed I'd forgotten to put my fleet's logo on my newest Boff's uniform (a male Caitian).
It was then I noticed the option to display the Fleet Emblem was missing from the tailor's options. At first I though it was a bug with Caitian Boffs until I noticed all my male Boffs were no longer displaying my fleet's logo.
After looking at the options for all my Boffs I noticed that all the females still had the option to display the fleet emblem, but all the males no longer did.
Hmmm interesting. I am actually using the Enterprise Mirror Universe uniform on this character. Although I've never noticed the lack of a Fleet Emblem on my male Boffs before (although tbh I often forget to put the Fleet Emblem on my uniforms and I end up having to go back and add them as I notice ).
I just tested this by changing my Male Boff's uniform jacket and you're right the Fleet Emblem option came back