In one of the new photos especially, I'd agree the back half looks like C.paleatus, but the front half doesn't! LOL. In shape, yes, but very dark head colouration in this one.
The missing eggs will have been eaten, and the ones that look as though they have a cloud around them are likely fungused, which often happens. But they don't appear to be fertile, and given that C.aeneus and C.paleatus can't interbreed anyway, they're not going to be fertile, I'm sorry.
May I ask what size tank it is? There's a bit of a dilemma here in that corydoras are a social fish that really need to be in groups of six or more. But paleatus prefer cooler water, which your betta wouldn't love (I have no idea about freshwater clam care I'm afraid) so while I'd usually suggest getting some more aeneus, assuming the tank is large enough, I wouldn't in your case since your current one is deformed, and it's really much better to avoid any chance of breeding from that one. So I'm torn on what to recommend.
@Byron , any thoughts here?