my DS attends a specialist SEN school that is designed for kids who may be a flight risk, the grounds are completely locked down during the day.. and they managed to 'lose' him for an hour on thursday because he was upset and 'hid' (not in a cupboard, just in an out of way place not immediately visible on general looking)
When he was in mainstream he needed a 1:1 and you have to careful about how its specified on the EHCP. 25hrs is lesson time only, it'd be 30+ if it includes breaktime supervision. DS managed to get away from his TA a couple of times by rabbiting quicker than she could follow, i never blamed her or the school, it happens.
If your child hid, then refused to come out when being called, then yes you can ask how he managed to slip notice, as that is definitely a failure on their part, however, his SEN is not an excuse for poor behaviour, there needs to be some level of personal responsibility for hiding for that long from the staff just because he didn't want to go to assembly.
I've had a good talk with DS about what happened thursday, and told him quite firmly that hiding from the staff isn't ever ok, and if he's struggling/feeling overwhelmed, he needs to talk.
As an afterthought, what my sons mainstream school did in the end was provide a small 'safe space' for him, which was actually a cupboard they appropriated into a calm room with soft lighting and beanbags, so if ever he felt overwhelmed, he had a specific place to go to.. it saved on him bolting to random places!
By all means keep your son home until you've spoken to the school, and made a plan for his safety going forward.. and do make an official complaint, but don't pull him out entirely, that serves neither of you at this point... you're better looking for a managed move with support if you genuinely don't think the school he's in is right for him.