Love this series so much.

so much work

This made me realize how nice it could be with yukkuris as pets. Especially koyukkuris lol

How about toilet training?

Yukkuri's don't need to excrete in all stories, its up to the artist to decide whether or not they need too.

The general consensus is "They don't have to excrete unless overfed / fed dry and dense food." There are exceptions, though.

Its actually less consistent though, its really up to the artist to decide.

How to they breed?

That varies by the artist. Either by rubbing together, regular copulation or filling exchange of any way. Babies can grow on a stalk, be born, some artists even draw them laying eggs. It's hugely inconsistent, I'd say 50:50 for rubbing/copulation.

I thought they would give birth normally though hard labour.

No, in this case, they automatically germinate after six months.