Dependent on when the Stripe account was created, fees may or may not be charged for security deposits and refunds.
For Stripe accounts created BEFORE September 14, 2017:
No - When issuing a refund against any payment collected by Stripe, Stripe will include their payment processing fee as part of the refund.
For Stripe accounts created AFTER September 14, 2017:
Yes - Stripe changed their policy for newer accounts and will charge their processing fee as part of the refund.