Even if your AFMU did itself get to 0% integrity somehow, a reboot/repair would generally fix it enough to let it rebuild your other systems, so in that sense you only need one.
On the other hand:
- hull repair limpets can be delivered from another friendly ship; AFMU function can't, and is more likely to be needed. You also need to potentially give up two internals (controller, small cargo hold) for hull repair. So if you only have two spare internals for repair tools, two AFMUs is probably better than limpets+controller and no AFMUs. If you had three spare internals, then sure, AFMU+cargo rack+controller is the more flexible option.
- AFMUs have the nice combination of: inexplicably massless, potentially not completely useless in deep space, can take damage. So that means that AFMU+AFMU is better than AFMU+empty (so long as you keep them powered down when not in use, of course) because the second AFMU can be an extra sink for module damage that might otherwise hit something important.