Basically they are the same meanings. But if you have to say there are some differences, you can read below:
你在哪所学校就读（the person you ask is already in some specific school)
你去哪个学校/你去什么学校（the person you ask maybe is planing to go some specific school,but he doesn’t get the offer yet or he does get the offer Alfreda, but doesn’t register yet ）
在：is (being)
去：is going to
Basically they are the same meanings. But if you have to say there are some differences, you can read below:你在哪所学校就读（the person you ask is already in some specific school)你去哪个学校/你去什么学校（the person you ask maybe is planing to go some specific school,but he doesn’t get the offer yet or he does get the offer Alfreda, but doesn’t register yet ）在：is (being)去：is going to
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