Your question on splitting students amoung many courses than having then in one, No, there is no difference.
For the other questions about performance, there is a dedicated forum called Hardware and performance: https://moodle.org/mod/forum/view.php?id=596. There is some starting pointers on its entry page. The full information appear only when you start a new discussion: https://moodle.org/mod/forum/post.php?forum=94. Go though them. In the mean time you may request the moderator to move your enquiry to that forum.
Hardware and performance
Same/Different Moodle courses
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