yeah, tray filled with water? Almost never is it a good idea to leave plants/soil sitting in water.
RE growing new plants from roots. You mean pieces of root you pruned off the main bunch? Not a chance. If you had cut the whole tree off at the base, the whole bottom bunch of roots MIGHT regrow new tree (or might not), but the top part you cut off would die. If you want to propagate it, you can take cuttings if the tree you have is mature enough:
You should take the cuttings November through January off of one-year-old wood.� One source said the cuttings should be six to ten inches long while another source suggested cuttings of twelve to twenty inches in length.� Treat the cuttings with a growth regulator and let them develop some roots in a greenhouse before planting in the spring.� The cuttings are the best way to keep the properties of the original cultivars
https://www.ndsu.edu/pubweb/chiwonlee/pl ... format.htm
Each winter when all the leaves have fallen from this deciduous tree, I create hardwood cuttings from the numerous suckers, or new shoots, which grow from the base of our trees. The pomegranate has a strong tendency to produce suckers from its base and trunk. Because of these numerous suckers, a pomegranate tree without annual training and pruning naturally develops into a large shrub. These suckers are perfect for hardwood cuttings in that they are straight, vigorous, and have plenty of buds, or new growing points. With my hand shears, I cut them about twelve inches long and plant them eleven inches deep to prevent them from drying. The next winter I can dig them up as bare root trees and plant them in their permanent locations. If kept cool and moist, newly collected cuttings can be planted weeks later.
https://patch.com/california/ramona/bp-- ... s-eb34119b
But of course your bonsai probably doesn't have 6" long shoots and I don't know if the bonsai suckers the way the full sized ones do.