Does breeding two pets change their value(mainly, decrease the value of a rare pet)?

It tends to decrease the value, specifically of tagged themed pets. The reason for this is that once a sylesti is bred it can no longer be gender swapped and you can no longer use a Philter of Trait Disruption (Themed) on it.

Something else that lowers value that newer people tend not to know about is mutating. If you're considering selling a tamed sylesti, you're better off not mutating it first. Being able to use a greater mutator to add a trait of the buyer's choosing is a big plus, so not being able to do so can take away quite a bit from a pet's value.

So, i guess i shouldn't breed my Dark Love Sylvorpa(unless only female pets lose value?), but find another male Sylvorpa instead(or, ideally, two: a male Cool Night Sylvorpa to breed with my female one, and an ordinary male Sylvorpa to breed with my other female Sylvorpa)?

Also, would breeding make much of a difference with other pets(ones that aren't worth much to begin with)?

Well, since the reason pets lose value from breeding is because then they can't have their gender swapped or their traits rearranged by the trait disruptor (for tagged themed pets), it lowers the sale value of both males and females. If you're not planning on selling, but instead on breeding the pets toward a goal, then you don't really need to worry about whether or not breeding will lower the value. Whether breeding makes a difference or not in value is really a call made by the individual buyer, otherwise.

Also, when replying it's best to hit the little @ at the bottom of the post of the person you're replying to. Then they get notified about the reply you made ^.^