I think it mostly depends on what would be funnier or cooler. For example, I did a co-mission last year in which one of my Agents, Luke Celinus, appeared. He has an eye missing from an accident several years ago, and his temporary partner (an old friend of his) pranked him to give his disguise two eyes. This led to hilarity as he tried to cope with suddenly having a completely different field of vision again and kept bumping into things.

Remember, the PPC runs on the Rule of Funny and Rule of Cool.

I forgot what her name is, and I don't remember how she dealt with this issue. I think it made it possible for her guide dog to talk.

Perhaps someone else knows who I'm thinking of.

A while back, though, there was a question about whether the disguise generator could actually make the agent into a different species, or whether that was more of a projected image. I believe the answer was yes to the first half. So, logically, disabled agents can set the DG to not have a disability in their disguise.