I have an algorithm that uses QRAM, after accessing the given QRAM that store M d-dimensional classical vectors, the state of the index register and the data register become entangled. But for now I don't have the QRAM black box, I just initialize the state of both systems by providing an array value to the registers at once using initialize function that exists in the qiskit module. My question is I have assigned the value 0 for non-visible basis. Is that ok?
If you are talking about the qRAM for encoding real numbers in amplitudes of a quantum system yes. Basically, you assume without loss of generalities that your problem/vector is of size a power of 2. But if your problem is not exactly of this type, we just pad with 0s. When you apply a quantum algorithm, you just need to be sure you are doing the computation you want.