Democracy is a political system used by meat-based, baseline humans, who are all fundamentally very similar. The greatest variation is that between Einstein and the village idiot, but 99% of people are far from either extreme.

One of the key ideas leading to democracy is equal rights. It makes sense to give all humans equal rights because their abilities, needs, and desires are really very similar. But ems inhabit a far greater class of possible behaviors, abilities, needs and desires. It's not clear to me why it even makes sense to consider a democracy of ems.

Another problem is that, as you point out, a one instance-one vote system would create a huge artificial restriction on the creation of legal copies. Creating copies is probably very desirable for anyone rich enough to run them. So the only possible outcomes are either a huge majority of disenfranchised copies created without a license, or else a huge illegal underworld of copies that is brutally repressed by the government because, once a copy is created, they have to grant it full rights.

Just look at the state of modern copyright (and patents) - a huge artificial legal restriction on the proliferation of software. Then imagine copyright applied to sentient beings. Enforcing a system of government licensing of em copying would mean enforcing the non-existence of free software and open hardware, or any software or hardware free from government control.