Roundworms are actually pretty cool, you can kill them off, and all the signs will go away, but they lay dormant in the muscle and when a bitch becomes pregnant they activate. Most puppies will get round worms from their dam, and we worm dam and pups without a fecal, just as a matter of course.
Hooks do not shed eggs all the time, so the pups and the bitch can have hooks and you might not know it. Hooks are scary because they attach in the intestine and cause bleeding. In young puppies that can be bad. Round worms can be bad too because they can cross over to humans, and kids with rounworms can actually go blind. So, it is nothing to fool with, as I am sure you know. I am surprised that your vet will not worm a litter without a fecal. In my opinion, that is asking for money. All puppies should be wormed.
There is another micro-organism that you might want to consider looking for if the pups develop a loose stool, and that is coccidia. Albon takes care of it, but if puppies develop diarrhea it can be very dangerous as they dehydrate quickly.
Again, I think you are doing great. Now is the point where you almost have to clean that box at least twice a day and I layer papers so I can snag them out when I see messes. As soon as the pups start eating solid food, the dam may or may not clean up after them as much. Puppies are filthy things really. They will roll in poo when they are playing, walk in it, and then walk in their food or water dishes. They love to tumble in their water dish.
I had some hag give me the up-turned nose because my play yard outside had bottles hanging instead of bowls down. Well, bowls tip, get walked through, etc. The bottles at least ensure clean water for the puppies. But whatever. Again, being able to move the pups from one area to another, clean and disinfect the other area completely and then move them back makes things somewhat easier.
There is really no help for it. Puppies will need baths at some point. As I said, there is just no way to completely eliminate the chance of them rolling in gross yuck. When they are really little, I use the kitchen sink, easier on my back, and if you have one of those little sprayers, it makes it easier to rinse them thoroughly. Then wrap them up in a towel and dry them good. It is at this point I get out the clippers and clip their toenails. Be sure you have stypic powder on hand, as if you nick a quick you will want to stop it from bleeding. Flour works, but not as well. Try not to make a big deal about it if you do nick one. Do everything matter of factly.
Also, I always worm the dam when I worm the pups. She is cleaning up after them, and well, she reinfects herself, so I just go ahead and do it. Strongid or Nemax is safe.
Jenna, RN CGC & Babs, CD RA CGC HIC
Heidi, RA CGC
SG3 Odessa, SchH1, Kkl1, AD
Ninja, RN CGC & Milla, RN CGC
Joy, Star Puppy, RN CGC
Dolly CGC & Bear CGC