Nematodes are structurally simple organisms. Adult nematodes are comprised of approximately 1,000 somatic cells, and potentially hundreds of cells associated with
the reproductive system . Nematodes have been characterized as a
tube within a tube ; referring to the alimentary canal which extends from the mouth on the anterior end, to the anus located near the tail. Nematodes possess
digestive, nervous, excretory, and reproductive systems, but lack a discrete circulatory or respiratory system. In size they range from 0.3 mm to
over 8 meters. I personally say try to get rid of the nematodes.
As for picking up the waste on the tanks substrate
gently tap water surface before putting my syphon in that location any fry near by swim away.
They will keep away from big water movement like syphon makes for fear of being eaten
I have a bucket+see through jug that are only for aquarium use to avoid soap residue ect.
When I have new fry my cleaning takes a little bit longer as I check every jug for little fry before emptying into bucket. If I see a fry in jug I gently release jug water back into aquarium with fry.
When refilling my aquarium I only pour water in one location+have noticed fry stay at opposite side of tank out of harms way.
Make sure you break up food into find dust for fry until they get bigger+can manage to eat norm food