I have definitely seen conditions like this before - not to often but they come up. The last kitten I saw with this issue actually had pyometra (an infection of the uterus). Yikes! But there are a variety of causes. Puppies can often have a sterile vaginal discharge, but it's less common (therefore more concerning) in kittens. I usually do cytology (take a sample of the discharge, look for evidence of what is going on). If there is bacteria I begin with antibiotics that are safe for that age range quickly, and a culture of the sample as well if we are trying to avoid going to a spay. But yes…often an early spay can both determine the cause and eliminate the discharge. That's often something that is done.
P.S. - Thank you for taking in the kittens. The world needs more people like you.