I'd imagine the devices between the MACSEC Switches are going to struggle to correctly pass on the traffic.
As far as I know the entire frame payload in encrypted, this payload will make no sense to an upstrem device not running MACSEC.
The easiest solution, if I were you, would be...
Get the two MacSec Switches working in the lab, back to back with a fibre or ethernet connection, so you can fully confirm your configuration is correct.
Make sure you are happy they are communicating freely.
Then place your devices, hubs etc between and see if things break.
The fact that the netgear switch works at all is surprising.
I don't see how you are going get this working across a wireless link thought !!
Regards to your second question - yes spanning tree CDP VTP are all supported - once the switches are directly connected.