At ds1's previous school, all the boys had to have a load of expensive PE kit, that you could only buy from the school, plus football boots and two pairs of trainers. Most of them also had the school kitbag, and since the lockers were too small for the kitbags, shelving was provided around the school, for the kitbags to live on (they weren't allowed to take their kitbags into lessons). It was a common occurrance for someone to pick up the wrong kitbag and, when they discovered their mistake, to just dump the bag on the nearest racks, rather than bothering to take it back to the rack they'd got it from - so some other boy's kit would be missing, and he'd have to search the whole school for it.
It was also considered a huge joke to take someone's kitbag and hide it, or even to take everything out and hide all the items in different places round the school - which was an utter nightmare if this happened to you. And it happened to ds1 twice! The second time, the bag wasn't found for months and months - by which time we'd had to spend over £100 replacing his kit - and it would have been more if we hadn't bought cheap trainers and footie boots in case the same thing happened again. The bloody rugby socks at that school were £6.50, and they had to have indoor PE kit, outdoor PE kit and rugby kit - all only available from the school.
I was very cross indeed about this - I didn't see it as a joke - I saw it as theft, and told the Headmaster so - but as far as I could see, the school couldn't have cared less about the issue. It was never even raised as a 'this isn't funny, boys, don't do it' in assembly.
Oh - and he had his shoes taken off his feet and hidden - again, another 'prank'. One shoe was found, but the other never reappeared, so we had to buy a new pair - so I can understand your anger, OP.
My line with the school would be that your son had taken all possible care of his shoes, and that as they'd they had vanished whilst he was out doing PE, he cannot be held responsible for their disappearance - and that the school should be investigating to find out what has happened to them - tbh, it sounds like more of the same bullying, and the school are clearly not dealing with it.
You and your son have my sympathy. And well done for sticking up for your son re. the bullying - it's more than my mum did for me (which has blighted my life - the fact that she dismissed the bullying was a worse betrayal, imo).