Shooting in the dark here, but what happens if you try...

input.1.joystick.0.axis.0=JOY1_HORIZ.0
input.1.joystick.0.axis.1=JOY1_VERT.0
input.1.joystick.0.button.0=JOY1_FIRE_BUTTON.0
input.1.joystick.0.button.1=JOY1_2ND_BUTTON.0
input.1.joystick.0.button.2=JOY1_3RD_BUTTON.0
input.1.joystick.0.button.3=JOY1_4TH_BUTTON.0
input.1.joystick.0.button.4=JOY1_5TH_BUTTON.0
input.1.joystick.0.button.5=JOY1_6TH_BUTTON.0
input.1.joystick.0.button.6=JOY1_7TH_BUTTON.0

According to the E-UAE joystick docs, it should be able to use all of these buttons. However, it also says you'll have to boot with a CD32 rom to make them available.

https://github.com/keirf/e-uae/blob/master/docs/joystick.txt