The simple (though entirely unfounded) answer is that obviously both culture and 40k universes have comparable souls. The reason why cloning is such an issue in 40k and not in the Cultureverse is that Souls have some kind of connection to the warp.

If the warp was ever made calm again, cloning might actually be possible without horrendous, 40k-genre-appropriate consequences.

The culture's own faith in it's own science and scientific superiority stills the warp selectively, just enough for their own science to function unaffected by this, at least when they use it in their own ships and so on.

(It'd be interesting to, say, have the RT try using the culture's cloning stuff only for it all to go horribly 40k style wrong due to this vital difference).