Is it permissible, Islamically, for a father to evict his paternal uncle and the uncle's wife from the house he lent them in 1999, especially given the uncle's and his wife's procrastination in vacating the house and their misuse of money? And is it permissible to supplicate for their departure from the house due to the material and moral harm they inflict?

Your father is to be praised for helping his brother by granting him the house, and he will receive reward and recompense from Allah for that. If your father wishes to reclaim the house from his brother, he has the right to do so. As for you, you do not have the right to reclaim it without his command. His brother ought to consider your father's circumstances and return the house to him. There is no harm in supplicating against the brother or his wife for vacating the house, as long as it does not involve sin or the severing of kinship ties.