@Lem13 Just make sure your Apple hubs also connect to main wifi and other devices connect to your IoT network (not guest network, guest network has AP isolation so devices on this will be auto isolated). I have devices on IoT network and they communicate just find in HomeKit.

  @Espress0-0 thanks for responding.  I have 2 AppleTVs hard wired to the Deco and 3 Home Pod minis connected to the main network. All of my Hue lights show up on HK, but the Hue bridge is hard wired to the Deco.  I have a few Meross outlets, Eve sensors and a Netatmo weather station that are all HK compatible, but the installations of these all forced me to use the main network. I guess if I connected my phone to the IoT network instead of the main network before installing these devices, I could have put them in the IoT network instead.  

The only devices that are now working properly are my Ecobee thermostats.  I was able to install them onto the IoT network despite my phone being on the main network.  At first, they didn't show up HK despite adding them through the Ecobee settings.  I removed them from HK and readded them, and now they work.  
 

The main issue I still have is that I have several Wemo switches and outlets that won't show up on HK. They are all connected to the IoT network and the Wemo bridge that gives HK compatibility is wired to the Deco. I've tried removing and readding the bridge several time, but nothing.  I've also tried the Homebridge plugin that I was using on my old setup and it doesn't work either.  
 

I have several Wyze devices connected to the IoT network and using Homebridge and these don't show up either.  All this worked fine on my old Mesh router, but that didn't have a similar IoT network.  
 

Any further suggestions?

  @Lem13 Did you reset those Wemo/Wyze switches, I don't have any of them but I do have a bunch of Meross smart switches installed. I know Meross is very finicky about connecting to wifi, the only way for me to get them on my 2.4Ghz wifi only is to connect phone to 2.4GHz wifi and disable auto join on the 5Ghz main wifi before setting them up. The other suggestion is if you can reset the Wemo/Wyze and check in HB plugin if there is any option to change UDID for those devices, I had to do that when re-adding my Samsung TV to the Samsung Tizen HB plugin as HomeKit not be able to detect the TV again once added. If that's not the case try removing cached accessories for Wyze/Wemo in HB, uninstall and install those plugins again. I don't think there is any settings on Deco mesh side you have to do, as Apple use mDNS to discover HomeKit devices, I'd focus more on troubleshooting HK devices within HomeKit itself or HomeBridge.

  @Espress0-0 Thanks again for the reply.  I realized that I had the IoT network setup for both 5GHz and 2.4GHz, so I shut off the 5 thinking that might be the cause of some of the issues, but it's not clear. I also realized that in some cases, I need to have my phone connected to the IoT network when adding devices in order for them to be connected to the IoT network.  Otherwise, they default to the main.  But for some devices, such as the Wemo and Wyze, I can select which network to connect them to regardless of what network my phone is on.  
 

I removed all my Wemo devices and reconnected them, but I still can't see them on HK. HK sees the Wemo bridge, but doesn't have any affect.  There's only one Wemo device it sees, but that's a HK compatible Wemo Mini plug.  I deleted the Wemo Home Bridge plugin because the Wemo bridge always worked before I installed HB, so I'll try reloading that to see if it works.  Unfortunately, HB is not letting me install (or even locate) new plugins, but otherwise seems to be working, so I have to figure out what's up with that. Will probably just do a brand new reinstall on it.  
 

Otherwise, the new Deco seems to be working ok.  It's definitely solved some of the issues I had with my old Orbi, but still unsure on these new issues.  Another oddity is that several connected devices often show up on the list of offline clients and I can't figure out why.  They seem to work properly.  The Meross outlets are a good example.  Are the going off wifi and working through the Matter bridge?  Two of my Wemo switches are doing this as well and they definitely aren't Matter devices.

  @Lem13 Hey I don't have any Wemo devices to test out for you, but I can give you some insights about online/offline devices in Deco app. In general, Deco app reports somewhat exactly the online/offline devices but I find it not quite accurate so I barely look at them. I only rely on the total number of devices that Deco showing, when there are a very off number (i.e it only shows 20 connected while I know I have 80 devices) then there could be some disconneced nodes. That was before I set up my own Uptime Kuma server to track for online devices, basically it will keep pinging the specific device/host and when it cannot ping that device it will send me a notification about that. I have seen some decices reporting offline in Deco but still ping-able and vice versa.