Placing a condition that is illegal in a contract does not legitimize it. If confiscating and keeping an item is stealing, then it cannot be included in a contract. That clause does not make it hefker or generate yiush. It does reflect on the morals of the one who demanded it. It also points to the bullying that occurs in the contracts with yeshivos, where we parents are forced to agree to prevent our children from being rejected or refused.
Iced: I worked for the Dept of Ed. There was no policy about cell phones as you described. In fact, the suggestion to ban cell phones was rejected by all the leaders in the Dept and the NYC government because doing so would prevent children and parents from communicating in case of emergency. 9/11 was the demise of that suggestion, and it has never passed muster since then. We were allowed to take the cell phones, but to return them at the end of the school day. If the infractions were more serious, we were allowed to notify parents that the phones would be returned to them, not the child.
Here are a few direct quotes (translation mine):
ספר שכר והענשה בחינוך - הר"ר מאיר מונק - בהסכמת הר"ר שמואל הלוי וואזנר שליט"א
It is the right of the mechanech to confiscate a toy that is being played with during the shiur, and it is his obligation. But there are different ways of taking it. It can be taken with grabbing and anger, or it can be taken in a pleasant manner...... It is proper to set a date to return the object, Friday, every Rosh Chodesh, or the end of the term. If it is an object that should not be returned to the child, it should be given to the parents with the message that they should insure the child does not bring it to school.
ספר מלאכת ה' על הלכות מלמדים - הר"ר ישראל יוסף ברונשטיין - בהסכמות הרבה גדולי א"י
(Free translation) The question is posed whether the mechanech confiscating is muttar, since the issur of genaivoh applies to children as victims just like adults. If the assumed heter is that it facilitates limud haTorah, it falls with the category of מצוה הבאה בעבירה, and it is forbidden. The Mishneh Halachos (From R' Menashe Klein ZT"L) says this is not technically stealing because of the responsibility of the melamed. However, to confiscate an object with no intention of returning it, is assur.
In the above references, the issue of whether this "chinuch" actually teaches a negative lesson (teaching the child that stealing is permissible) is not addressed. That is addressed by R' Moshe Feinstein ZT"L, which is the basis for his psak to not take it.