Assalamu Alaykum,
The Scholars of Islam who were upon Quran and authentic Sunnah are unanimous that it is not permissible to say Ya to anyone who has passed away. Ya means "Oh" in English
Those who say Ya Ali, Ya Muhammad, Ya Hussein, Ya Abdul Qadir al Jeelani etc... are making sin. . for they are calling upon the dead to aid them. Or they believe the dead can hear the living. Which goes against the Aqeedah(creed beliefs) of Muslims
We should only ask for help from Allah (subhana wa ta'aala) and not to any of the dead or living.
Ya is used in Two permissible situations:
when you are calling someone who is alive and near you, i.e. ya abu fulan, ya Mabsoot, ya sidi3ee come here.
And of course, when we ask God for help, so we use Ya in our prayers. Ya Allah. Oh Allah. Ya Rabb.... Oh Our Lord
So, indeed when Sami Yusuf says Ya Muhammad, or whatever he is saying incorrect statements. These sorts of things are used by some deviant sects.. and is not from true Islamic belief. At Same time, we do not label anyone or say anything bad against someone as it is not our position to do so.
Asking Help and Calling upon Other Than Allah is Shirk
Wasalam.