So, any ingame way to tell if you caught all nexomon in an area?

[Hex: Onii-Chan]

I can't find an answer anywhere to be honest. Or are you just supposed to hope you have encountered everything and move on?

[Claymore]

You do have a kind of pokedex deal to see what you've caught, but sadly to ensure you've 100%ed an area in terms of what you can catch you'll have to use an external guide. https://platget.com/guides/nexomon-extinction-location-guide/ is an example (sorry, had to edit for the correct version).

https://pokeoneguide.com/nexomon/nexomon-extinction-maps/ for maps/mobility.