Would a son's disobedience to his mother in not raising the rent of an apartment inhabited by her husband (the uncle) be considered an act of defiance towards her, especially given that the paid rent is low and the tenant is her husband (the uncle)?

If your uncle's rent for the house is less than the market rate, you have the right to request that the rent be raised to the market rate. He is not permitted to rely on the family relationship to pay a low rent unless you agree, because a Muslim's property is not lawful except with his willing consent. Seeking this right is not an act of disobedience towards your mother, even if she does not approve, and she has the right to waive her share of the rent for your uncle. It is advisable to be gentle with him and consider the family relationship by reducing the rent in a way that does not harm you, as this falls under maintaining kinship, showing righteousness, and doing good.