First of all, the waqf get abused in daytime too, so what are you going to do now? Close the masjid during daytime? Also, books are taken away during prayer times too. And what would a homeless person searching for money do with books of hadith and qur'an? This is no argument.
You are stating yourself that they don't pray so what are they going to do with Islamic books? Besides, these books are taken away during daytime too simply because people do not understand the rulings of waqf or it is not mentioned clearly that books are supposed to stay in the mosque.
About breaking down sadaqa boxes. You simply take the money outside before the night they sleep. SIMPLE.
I am not saying you are supposed to sleep everyone and making it a camping place. But brothers who even PRAYED salah with us are turned down!! And even if they do not pray, why not let brothers talk to them first about the importance of prayer? Why kick them out immediately? Also, most of the mosques have rooms NEAR the mosque, like classrooms. Even in such rooms they are not allowed to sleep, where nothing can happen and nothing can be stolen! How is that possible? What kind of sick attitude can a Muslim have to tell him to go to the church or let him sleep on the streets in the cold? Tell me HOW please.