Why does the ship in Dead Space carry babies?

You are talking about enemies called Lurkers, their page on wiki says the following:

They are usually created from human babies and infant-like organ banks used in biological prosthetic procedures, but can also result from infected dogs, as is the case of those found onboard Sovereign Colonies ships and the icy surfaces of Tau Volantis.

So in case of Ishimura I'm afraid the answer is they are from "infant-like organ banks used in biological prosthetic procedures". Sounds really creepy even without necromorphs. Why they needed that many of those? Idk, when you mine with plasma cutters some limb-cutting incidents may occur indeed.