Yes, the Switch Port Mapper can discover your switches and show them in a list, as long as VPN allows network access to those switches via the standard SNMP protocol. Of course you would need to specify the read community to discover the switches. It acts like a password and is usually set to "public".
To try these features, download and run the trial version from the
Switch Port Mapper page.
Then, in the main menu go to
File - Manage Devices - Discover and enter your switches IP address range and a community string. The software will then discover all switches that respond to this community string.
Regarding disabling and enabling individual ports, there isn't currently such functionality in the Port Mapper. We are planing to implement some management functions in the future, but for now you could use an external tool like SSH or snmpset to do that.