Yes, it will affect the quality of isolated mitochondria.
Sucrose is used to maintain osmotic strength of the buffer while having low ionic strength. Addition of sucrose makes in and out of the cell isotonic. Storing isolated mitochondria in storage buffer containing isotonic sucrose will help to depress the increase in osmotic fragility during preservation. The functional activity (for example, membrane potential, etc.) of isolated mitochondria is well preserved.
On the other hand, PBS or DPBS could have an impact on the ionic and water fluxes across the inner and outer membranes of the isolated mitochondria thereby altering the composition of matrix and influencing the morphology of the organelle at large.
Storing isolated mitochondria in buffer containing sucrose is always preferred.
Malcolm Nobre Thank you for your response. I read that sucrose interferes with Protein quantification using BCA assay. Would you happen to have recipe for a storage buffer as the kit I use to isolate mitochondria doesn't come with one.