I can help you with the first half of your request--if you have NCM.
Just create a new NCM Job. Select the nodes against which it should be run, create the exact script and syntax you want run against them, and either fire it off manually or run it as a scheduled job.
What you do with the output . . . well, that's the part I'll leave to you. Share your ideas, please?
With the release of NPM 12.2 they have began to use CLI polling for monitoring Cisco ASA devices - there is no way to poll some information (Cisco AnyConnect users for example) from an ASA using SNMP for security reasons. I do not think that you can do your own customization and set up a UnDP CLI poller yet but I will explore this since I also have looked for this type of solution in the past. I will let you know if I find anything that allows you to create a CLI poller for other devices.
This at least lets you know that they are expanding their polling methods beyond SNMP. FYI, they already support the VMware API for polling ESXi Hosts and vCenter servers and SAM uses components that use perl to perform queries from the shell on Linux type servers. Those are the ones I primarily use but there might be other non-SNMP polling methods as well.
To help with your original issue, it might help to perform a snmpwalk against the two routers and scan through the values looking for responses that might be for NTP. I usually do one snmpwalk using the defaults to search the OID names and another snmpwalk requesting the numerical OID strings so that I can more easily identify the OID to use in the SolarWinds UnDP application.
Just in case you are not familiar with the snmpwalk syntax here are the two commands I always use (run from a Linux box)
snmpwalk -v 2c -c snmpstring 01.02.03.04
snmpwalk -v 2c -c snmpstring 01.02.03.04 -Ofn .1
I was looking through some settings and I did find that they added a CLI Device Template setting in the Edit Node Properties window. They allow you to edit the templates (via cloning) and apply them manually to a node as well, though automatic application is the default based on node's System OID value. I have not updated the template and applied it to a Cisco Node yet but it looks promising. I did not see this as part of the release notes for 12.2. I am not NPM 12.2 and SAM 6.5 - the latest for both as of February 13th, 2018.