Extra speed is more important than stealth when it comes to launching standoff munitions. Its not guaranteed that a CBG will be tracked all the time, so its good if the bomber can go supersonic if the CBGs position is different by a lot. Also Tu-22M3s wont only be used for anti-ship strike, but also tactical land strikes, and extra speed in case iads and radar net has been reduced through attrition is good, in order to escape ambushes. With extra speed the Tu-22M3 can scramble faster than a supersonic bomber and from an airfield further away from enemy cruise missiles, because It can fly fartjer for a shorter period of time. The other important factor is that the Tu-22M3 and Tu-160 can fly between both sides of russia faster, and bring standoff firepower faster from further away. If lets say a massed cruise missile strike destroys an airfield in the west(not likely but still possible), Tu-22s can be brought in like 4 hours from the far east.
Also, the fact that the Tu-22M3 can fly faster means that the booster stage of the hypersonic missiles can be smaller due to increased launch speed of the carrier.
Both the PAK Da and Tu-22M3 have their uses, and can complement rather than replace each ther.