In principle quantum communication has no side channels because side channels act like measurements, and measurements make it not a functioning quantum channel in the first place. So you need to have already solved side channel issues for basic function.
That said, wherever you convert the quantum data into classical data there will be potential side channels. For example, there have been attacks based on using a laser down the communication line to track the orientation of the measurement device at the receiver.
In general, the more you can do while the data stays quantum the better. For example, if you transduce the photon into a qubit inside a quantum computer, then the measurement can be hidden away inside the computer, instead of exposed to the communication line. And the measurement basis can be chosen after transmission arrival, instead of before.
The larger issue for most quantum key exchange setups is the transition from classical to quantum: you want not to accidentally generate two unentangled photons in the same secret polarization.
That said, wherever you convert the quantum data into classical data there will be potential side channels. For example, there have been attacks based on using a laser down the communication line to track the orientation of the measurement device at the receiver.
In general, the more you can do while the data stays quantum the better. For example, if you transduce the photon into a qubit inside a quantum computer, then the measurement can be hidden away inside the computer, instead of exposed to the communication line. And the measurement basis can be chosen after transmission arrival, instead of before.