We have multiple 802.1Q subinterface on Cisco Switches. The primary interface is showing the traffic but the subinterfaces don't show the traffic.
I think that's fairly common, even if you do a "show interface" and look at the subinterfaces they don't give you traffic, so I don't think it reports that via SNMP either. If you're doing L3 on the interfaces, you might be able to get something via Netflow? Not sure on that though...
Have you checked the boxes for Interface statistics for each of the sub-interfaces?
I don't have a Cisco handy in my home lab, but here's a screenshot of a device with subinterfaces:
These aren't always checked by default, so you may want to investigate.