I use 2 AEX's (5th Gen) to get better coverage in my house, but I can only setup guest network on the primary AEX
Yes, this is correct because the Guest Network will appear as as option when the AirPort is handling DHCP and NAT services.
The second one is running in bridge mode and creates dual networks with the same name but doesn't show any options for "Guest Network". I'm guessing that must be because it's in Bridge Mode maybe?
Correct again. It's a "Catch 22". In Bridge Mode, the correct setting for the second AirPort, DHCP and NAT are disabled, so the Guest Network option will not appear.
Is there a better network configuration that would allow me to have a guest network on both AEX's?
Unfortunately, no. Another way of saying the same thing is that the Guest Network cannot be "extended", either using a wireless or Ethernet connection between the AirPort routers.
If you would like to see an option to "extend" the Guest Network, you might want to let Apple know.
After doing some searching I see that Access Control settings for the primary network are also applied to the Guest Network. I've got an old AEX 1st Gen. that's just sitting around collecting dust. If I used it to create a Guest Network what would I need to be able to keep that network isolated so that it provided access only to the internet?
You would need to configure the AirPort to act as a router.....DHCP and NAT enabled....on a different subnet.
If you have not changed the DHCP range that your "main" network is using, all devices are receiving a 10.0.1.x IP addresses.
So, you would configure the "new" AirPort to use a different DHCP range.....say 10.0.2.x.
This will also create a Double NAT error intitially, which you can click to "ignore" and the indicator light will be green.
Clients on this network will have Internet access, but they not be able to "see" clients or devices on your "main" network, and vice versa. If you want the "guests" to be able to print, you will need to designate a printer for this network.
Post back if you need some help with this. Hopefully, you are using OS X 10.6.8 as your profile indicates, since this is difficult to do using Lion or Mountain Lion, and pretty straightforward using Snow Leopard or any of the 5.x versions of AirPort Utility.