Let me see if I can help.
The Hardwire Expander AKA Zone Expander connects to the OmniPro II via the 20 pin expansion buss connector using a short ribbon cable. It is usually physically mounted piggyback on the main board in the same enclosure. You can have up 4 expansion boards, but only 2 can be Zone Expanders. The others can be serial, ALC, etc. As the name implies each Zone Expander provides only 16 zones and no outputs. If you only need more zones and all of your wiring terminates at the main board this is a good choice.
The Expansion Enclosure connects to the OmniPro II via the console buss via a 4 wire cable. It may be located at some distance from the main controller and typically has it's own power supply and own enclosure. You may have a max of 8 Expansion Enclosures. Each Expansion Enclosure provides 16 zone inputs and 16 outputs. If you need additional zones and outputs, or you have several zone terminated at a remote location this is a good choice.
When I talk about zones terminating in a remote location I am referring to a scenario like a two story house where you bring all of your upstairs zones to an Expansion Enclosure located upstairs then run a single 4 wire cable from the Expansion Enclosure to the main board. Same sort of thing for out buildings as mentioned above.
So using an OmniPro II, you can have:
16 Zones on the main board
32 zones (2 x 16) on Hardwire (Zone) Expanders
128 zones (8 x 16) on Expansion Enclosures
Which gives you 176 zones.