In my medical office we ask patients not to use their cell phones in the waiting room. We certainly do not confiscate them but it is a courtesy to others who may need to be next to each other for a while. The yeshiva must contend with a comparable issue, that of unwelcome disruption which, without rules, could descend into disrespect for its classrooms and its teachers. Having completed my entire formal education before the invention of the cell phone, I can attest that it is quite possible to deal with urgencies without them.
The rosh yeshiva and the school’s governance have the right to set policy and enforce policy, which would include banning certain items and discreet search for contraband when its presence is seriously suspected. I think frisking a kid in the middle of the hall or doing a strip search at all would violate basic principles of avoiding public humiliation, that I hope every rebbe would hold in utmost regard.