Pregnancy is awesome, but unfortunately, it isn't that well implemented yet, as in you loose too much hp for sex scenes and your offspring aren't really much helpful.
It ends after the second boss, right?
To be honest, most of the damage can be avoided, but it is RNG dependant.
First of all, yes there is always a chance to get pregnant (except with a few enemies who will parasite Inesa instead, getting parasited will only give birth to an enemy). But there are better way.
For exemple you have a potion that put her into a state that increase her pregnancy chance massively, this effect can also happen randomly at the start of a floor.
A few relics can also help, some reduce damage taken during h-scene, another one heal you up completly when she gets pregnants.
But yeah, the problem is that all these solutions are RNG, otherwise you have to deal with the standard chance of pregnancy (I suspect it's influenced by a few things, like time since birth, ect... but I don't know for sure)
As for guardians (the name of the offsprings), they are determined by the kind of enemy that got her pregnant, some are relatively weak and slow, others are absurdly strong they can probably do as much damage as Inesa herself (the one from the farmer or the plants are quite good), and there is a relic to increase their damage and create another one for free.
As of right now, the game does have a 3rd part after the second boss, however the 3rd floor isn't complete yet as there is no boss (there is a BOSS ROOM, but only a bunch of random enemy).