I have not worked in secondary for about 7 years now but I never found a solution to this in the school I worked in for over 20 years. It gradually got worse as the years progressed.
Not allowed to take a shoe in return for a pen - fire hazard if there was a fire alarm (in any case I didn't fancy sharing a classroom with shoeless teenagers, and I included my own DS in that.) They honestly couldn't care less about ties etc and would point blank refuse to hand other stuff over. Once a colleague took a phone and the pupil sneaked it back and then accused her of stealing it.
Counting in and out was too time consuming and when I did try, they just outright lied that they had returned it or Johnny had taken it - or whatever.
Labelling didn't work because they would just set their minds to how to remove the labels and nick the pen, or would even take the pen with the label because they really gave zero shits.
Just refusing to lend equipment - Well I can't write then I can't do any work, I'll just sit here and disrupt and if you complain I'll just say all I needed was a pen.
Detentions - two camps here, parents who were mystified why their child didn't have a pen when they had checked their bag this morning and they had several (little buggers couldn't be bothered getting stuff out of their bag), or parents who refused to let their child do a detention for something as trivial as not having a pen. In any case, that was a detention I had to do too - and chase up.
After 20+ years of this I considered pens collateral damage and thought that even if they did steal them, if we were lucky it just meant that they had a pen for their next lesson. What was really depressing was to find the pens snapped in half (on purpose) and trodden into the carpet at the end of the lesson - and getting criticised by my line manager because the cleaner had complained.
Do I miss those days? Hmm ...?
I still have a bag of pound shop pens though - you never know. 