We still have old VMware Workstation 9 licenses. Can we upgrade them to the current Workstation 12 Pro?

Unfortunately, you can not do that. According to VMware, only Workstation 10 and 11, Player 6 Plus and Player 7 Pro are eligible for upgrade. As a Workstation 9 license owner, you must purchase a new license.

Source: Official VMware Workstation 12 Pro FAQ Website (https://www.vmware.com/products/workstation/faqs/licensing.html) Stand 2016-07-12