No I don’t think she will be Queen of Scotland if they get a ‘yes’ to succeed.
They can become a republic.... which means separate passports, separate financial system, separate armed forces, separate economy and they’d have to reapply for EU membership.
It’ll depend on how they’ll draft the new constitution, if the outcome is ‘yes’. If they go republic, then definitely she won’t be. Though so far some nationalists have said they’ll keep the present queen, but can’t guarantee long-term future of monarchy in Scotland. Why do you think they won’t keep her?
A ‘new’ Scotland would have kept the Queen. The RF is Scottish after all (despite most people thinking they are English or German).